SMTL ID : 7eda.1

Structure of monomeric photosystem II

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-mer

Ligands

1 x OEX: CA-MN4-O5 CLUSTER(Covalent)

OEX.1: 12 residues within 4Å: Chain A: D.51, Q.155, D.160, V.175, E.179, H.322, E.323, H.327, D.332, A.334 Chain C: E.332, R.335 12 PLIP interactions: 8 interactions with chain A, 3 interactions with chain C, 1 Ligand-Water interactions Metal complexes: A:E.179, A:H.322, A:E.323, A:E.323, A:E.323, A:D.332, A:D.332, A:A.334, C:E.332, H2O.1 Hydrogen bonds: C:R.335, C:R.335

1 x FE2: FE (II) ION(Non-covalent)

FE2.2: 5 residues within 4Å: Chain A: H.205, H.262 Chain D: H.203, H.257 Ligands: BCT.51 4 PLIP interactions: 2 interactions with chain D, 2 interactions with chain A Metal complexes: D:H.203, D:H.257, A:H.205, A:H.262

35 x CLA: CHLOROPHYLL A(Non-covalent)

CLA.3: 27 residues within 4Å: Chain A: F.109, Y.137, P.140, S.143, V.147, F.172, M.173, I.174, F.176, Q.177, I.182, L.183, H.188, G.191, V.192, V.195, F.196, V.273, A.276, A.277, I.280 Chain D: L.171, L.194 Ligands: CLA.4, CLA.5, PHO.6, CLA.52 16 PLIP interactions: 13 interactions with chain A, 3 interactions with chain D, Hydrophobic interactions: A:F.109, A:Y.137, A:F.172, A:F.176, A:Q.177, A:I.182, A:I.182, A:L.183, A:V.192, A:F.196, A:F.196, A:I.280, D:L.171, D:L.171, D:L.194 Metal complexes: A:H.188 CLA.4: 19 residues within 4Å: Chain A: V.147, F.148, M.162, I.166, T.169, F.170, F.172, M.173 Chain D: M.187, V.190, A.191, L.194, G.195, L.198 Chain K: L.30 Ligands: CLA.3, PHO.6, CLA.52, PL9.55 8 PLIP interactions: 2 interactions with chain D, 5 interactions with chain A, 1 Ligand-Water interactions, Hydrophobic interactions: D:V.190, D:L.198, A:V.147, A:F.148, A:F.148, A:F.170, A:F.172 Metal complexes: H2O.1 CLA.5: 21 residues within 4Å: Chain A: Q.189, V.192, A.193, F.196, G.197, L.200, F.201, W.268 Chain D: F.62, L.63, F.142, F.146, V.164, I.167, F.168, F.170, L.171 Ligands: CLA.3, PHO.7, DGD.50, CLA.52 13 PLIP interactions: 6 interactions with chain D, 6 interactions with chain A, 1 Ligand-Water interactions, Hydrophobic interactions: D:F.142, D:I.167, D:F.168, D:F.170, D:L.171, D:L.171, A:V.192, A:V.192, A:F.196, A:L.200, A:F.201, A:W.268 Metal complexes: H2O.1 CLA.8: 22 residues within 4Å: Chain A: V.25, I.26, P.29, T.30, F.83, Y.84, P.85, I.86, W.87, Q.103, L.104, F.107, H.108, L.111 Chain H: V.8, Y.9, V.11, V.12, F.15 Ligands: BCR.9, LMG.11, CLA.37 14 PLIP interactions: 10 interactions with chain A, 4 interactions with chain H, Hydrophobic interactions: A:T.30, A:F.83, A:P.85, A:I.86, A:W.87, A:L.104, A:F.107, H:V.8, H:V.11, H:F.15, H:F.15 Hydrogen bonds: A:I.86 Salt bridges: A:H.108 Metal complexes: A:H.108 CLA.13: 11 residues within 4Å: Chain B: W.184, G.185, P.186, F.189, V.207 Chain G: F.40, I.43, I.47, L.54 Ligands: CLA.14, RRX.62 10 PLIP interactions: 5 interactions with chain B, 4 interactions with chain G, 1 Ligand-Water interactions, Hydrophobic interactions: B:W.184, B:P.186, B:F.189, B:F.189, B:V.207, G:F.40, G:F.40, G:I.47, G:L.54 Metal complexes: H2O.1 CLA.14: 26 residues within 4Å: Chain B: E.183, W.184, G.188, F.189, P.191, G.196, V.197, A.199, H.200, A.203, A.204, V.207, F.246, V.250, T.254 Chain G: F.37, F.40, L.41, I.44, L.45, Y.48 Ligands: CLA.13, CLA.15, CLA.17, RRX.62, DGD.63 18 PLIP interactions: 12 interactions with chain B, 6 interactions with chain G, Hydrophobic interactions: B:W.184, B:F.189, B:P.191, B:A.199, B:H.200, B:A.203, B:A.204, B:V.207, B:F.246, B:F.246, G:F.37, G:F.40, G:L.41, G:I.44, G:I.44 pi-Stacking: B:F.189, G:F.40 Metal complexes: B:H.200 CLA.15: 24 residues within 4Å: Chain B: R.67, L.68, A.145, L.148, C.149, F.152, L.157, M.165, V.197, H.200, H.201, F.246, A.247, V.250, V.251, T.261 Chain G: F.37 Ligands: CLA.14, CLA.16, CLA.17, CLA.18, CLA.20, CLA.21, CLA.22 17 PLIP interactions: 15 interactions with chain B, 2 interactions with chain G, Hydrophobic interactions: B:L.68, B:A.145, B:L.148, B:F.152, B:F.152, B:V.197, B:F.246, B:A.247, B:V.250, B:T.261, G:F.37, G:F.37 Hydrogen bonds: B:R.67 Salt bridges: B:R.67 pi-Stacking: B:F.152 pi-Cation interactions: B:H.200 Metal complexes: B:H.201 CLA.16: 21 residues within 4Å: Chain B: W.32, F.60, F.64, R.67, L.148, V.244, A.247, A.248, V.251, F.450, H.454, F.457, A.458, F.461 Ligands: CLA.15, CLA.17, CLA.18, CLA.19, CLA.23, CLA.24, CLA.25 18 PLIP interactions: 18 interactions with chain B, Hydrophobic interactions: B:W.32, B:F.60, B:F.64, B:L.148, B:V.244, B:A.247, B:V.251, B:F.450, B:F.450, B:F.457, B:F.457, B:F.457, B:F.457, B:F.461, B:F.461 Salt bridges: B:R.67 pi-Stacking: B:F.450 Metal complexes: B:H.454 CLA.17: 29 residues within 4Å: Chain B: T.26, V.29, A.30, W.32, A.33, A.37, V.61, F.64, M.65, R.67, L.68, V.95, H.99, L.102, L.142, G.146, C.149, A.204, G.208 Ligands: CLA.14, CLA.15, CLA.16, CLA.18, CLA.21, CLA.22, CLA.24, CLA.25, CLA.27, BCR.31 11 PLIP interactions: 11 interactions with chain B, Hydrophobic interactions: B:T.26, B:V.29, B:A.30, B:W.32, B:A.33, B:L.68, B:V.95, B:L.102 Hydrogen bonds: B:M.65 Salt bridges: B:R.67 Metal complexes: B:H.99 CLA.18: 22 residues within 4Å: Chain B: L.68, G.69, V.70, W.90, V.95, A.98, H.99, V.101, L.102, L.105, L.148, G.151, F.152, F.155, H.156, F.161, G.162, P.163 Ligands: CLA.15, CLA.16, CLA.17, BCR.31 16 PLIP interactions: 16 interactions with chain B, Hydrophobic interactions: B:L.68, B:V.70, B:W.90, B:W.90, B:V.95, B:A.98, B:V.101, B:L.102, B:L.102, B:L.105, B:L.148, B:F.155, B:F.161, B:F.161 Salt bridges: B:H.99 Metal complexes: B:H.156 CLA.19: 20 residues within 4Å: Chain B: W.32, M.36, Y.39, T.43, Q.57, G.58, M.59, F.60, T.326, G.327, P.328, W.449, F.450, A.453, H.454 Ligands: CLA.16, CLA.25, BCR.29, UNL.30, LMG.32 14 PLIP interactions: 13 interactions with chain B, 1 Ligand-Water interactions, Hydrophobic interactions: B:Y.39, B:F.60, B:F.60, B:F.60, B:F.60, B:T.326, B:W.449, B:W.449, B:A.453 Hydrogen bonds: B:Y.39, B:G.327 pi-Stacking: B:F.60, B:W.449 Metal complexes: H2O.1 CLA.20: 20 residues within 4Å: Chain B: L.228, T.235, S.238, S.239, A.242, F.245, F.246, F.462, H.465, I.466, T.472, L.473 Chain D: L.25, I.112, M.115, L.116, F.119 Ligands: CLA.15, CLA.21, CLA.22 14 PLIP interactions: 8 interactions with chain B, 6 interactions with chain D, Hydrophobic interactions: B:A.242, B:F.245, B:F.246, B:F.462, B:I.466, B:L.473, D:L.25, D:I.112, D:I.112, D:M.115, D:L.116, D:L.116 Salt bridges: B:H.465 Metal complexes: B:H.465 CLA.21: 23 residues within 4Å: Chain B: F.138, V.207, A.211, F.214, H.215, V.218, R.219, P.220, P.221, L.224, L.228, M.230 Chain G: T.26, T.27, L.29, M.30, F.33, M.34 Ligands: CLA.15, CLA.17, CLA.20, CLA.22, RRX.62 10 PLIP interactions: 3 interactions with chain G, 7 interactions with chain B, Hydrophobic interactions: G:L.29, G:M.30, G:F.33, B:F.138, B:V.207, B:A.211, B:F.214, B:L.224 Salt bridges: B:H.215 Metal complexes: B:H.215 CLA.22: 23 residues within 4Å: Chain B: H.22, L.134, M.137, F.138, H.141, L.142, L.144, A.145, L.228, M.230, I.233, T.235, V.236, S.239, S.240, A.243 Ligands: CLA.15, CLA.17, CLA.20, CLA.21, CLA.24, CLA.27, RRX.62 10 PLIP interactions: 9 interactions with chain B, 1 Ligand-Water interactions, Hydrophobic interactions: B:L.134, B:M.137, B:F.138, B:L.144, B:L.228, B:M.230, B:I.233, B:T.235 Hydrogen bonds: B:H.141 Metal complexes: H2O.1 CLA.23: 22 residues within 4Å: Chain B: W.4, Y.5, R.6, V.7, H.8, T.9, L.237, I.241, L.460, F.461, F.463, G.464, W.467, H.468, R.471 Chain L: F.19 Ligands: CLA.16, CLA.24, CLA.25, CLA.26, LHG.57, LHG.66 21 PLIP interactions: 20 interactions with chain B, 1 interactions with chain L, Hydrophobic interactions: B:W.4, B:W.4, B:H.8, B:T.9, B:L.237, B:L.237, B:I.241, B:I.241, B:F.461, B:F.461, B:F.463, B:F.463, B:W.467, L:F.19 Hydrogen bonds: B:V.7, B:H.8 Salt bridges: B:H.8, B:H.468, B:R.471 pi-Stacking: B:W.467 Metal complexes: B:H.468 CLA.24: 23 residues within 4Å: Chain B: H.8, L.11, I.12, L.18, A.21, H.22, H.25, T.26, V.29, I.233, E.234, V.236, L.237, S.240, I.241, V.244 Ligands: CLA.16, CLA.17, CLA.22, CLA.23, CLA.25, CLA.26, CLA.27 19 PLIP interactions: 19 interactions with chain B, Hydrophobic interactions: B:H.8, B:L.11, B:L.11, B:I.12, B:L.18, B:A.21, B:T.26, B:V.29, B:I.233, B:I.233, B:V.236, B:L.237, B:L.237, B:L.237, B:V.244 Hydrogen bonds: B:S.240 Salt bridges: B:H.22 pi-Stacking: B:H.25 Metal complexes: B:H.22 CLA.25: 15 residues within 4Å: Chain B: H.8, H.25, V.29, W.32, L.460, F.461 Ligands: CLA.16, CLA.17, CLA.19, CLA.23, CLA.24, CLA.26, BCR.29, UNL.30, LHG.57 9 PLIP interactions: 9 interactions with chain B, Hydrophobic interactions: B:V.29, B:V.29, B:W.32, B:W.32, B:L.460, B:F.461, B:F.461 Salt bridges: B:H.8 Metal complexes: B:H.25 CLA.26: 18 residues within 4Å: Chain B: L.2, V.7, H.8, V.10, L.11, A.21, M.24, L.28, W.114 Chain K: Q.8, V.10 Chain L: F.19, L.23 Ligands: CLA.23, CLA.24, CLA.25, BCR.29, LHG.66 9 PLIP interactions: 7 interactions with chain B, 2 interactions with chain L, Hydrophobic interactions: B:V.7, B:L.11, B:M.24, B:L.28, B:W.114, B:W.114, L:F.19, L:L.23 Metal complexes: B:H.8 CLA.27: 20 residues within 4Å: Chain B: I.19, H.22, L.23, T.26, L.121, F.122, L.132, M.137, I.140, H.141, L.144 Chain G: L.6, L.10, L.13, N.14 Ligands: CLA.17, CLA.22, CLA.24, CLA.28, BCR.31 13 PLIP interactions: 8 interactions with chain B, 5 interactions with chain G, Hydrophobic interactions: B:I.19, B:L.121, B:F.122, B:L.132, B:L.132, B:I.140, B:L.144, G:L.6, G:L.10, G:L.10, G:L.13, G:L.13 Metal complexes: B:H.141 CLA.28: 14 residues within 4Å: Chain B: I.19, L.23, A.109, W.112, H.113, L.119, L.121 Chain G: T.4, W.5, L.6, G.7, L.10 Ligands: CLA.27, BCR.31 13 PLIP interactions: 9 interactions with chain B, 4 interactions with chain G, Hydrophobic interactions: B:I.19, B:L.23, B:A.109, B:W.112, B:W.112, B:L.119, B:L.121, G:T.4, G:L.6, G:L.10 pi-Stacking: B:W.112 Metal complexes: B:H.113 Hydrogen bonds: G:L.6 CLA.33: 23 residues within 4Å: Chain C: T.72, L.73, L.146, G.149, A.150, L.153, L.163, W.201, I.202, V.211, H.215, I.218, A.256, M.260, I.263, F.267, V.274, Y.275 Ligands: CLA.34, CLA.35, CLA.38, CLA.39, BCR.47 16 PLIP interactions: 16 interactions with chain C, Hydrophobic interactions: C:L.146, C:L.146, C:A.150, C:L.153, C:W.201, C:I.218, C:A.256, C:M.260, C:I.263, C:I.263, C:F.267, C:V.274, C:V.274, C:V.274, C:Y.275 Metal complexes: C:H.215 CLA.34: 25 residues within 4Å: Chain C: W.41, I.65, L.66, H.69, L.73, W.75, G.149, L.152, L.257, M.260, G.261, A.264, V.268, Y.275, L.404, H.408, L.411, A.412, F.415 Ligands: CLA.33, CLA.35, CLA.36, CLA.41, CLA.42, CLA.44 18 PLIP interactions: 18 interactions with chain C, Hydrophobic interactions: C:W.41, C:W.41, C:I.65, C:L.66, C:L.73, C:W.75, C:L.152, C:L.257, C:M.260, C:A.264, C:L.404, C:L.411, C:F.415 Hydrogen bonds: C:Y.275 Salt bridges: C:H.69, C:H.408 pi-Stacking: C:W.41 Metal complexes: C:H.408 CLA.35: 20 residues within 4Å: Chain C: I.38, V.39, W.41, A.42, T.46, L.66, H.69, I.70, L.73, W.75, V.92, H.96, L.257, M.260 Ligands: CLA.33, CLA.34, CLA.39, CLA.41, CLA.42, CLA.44 9 PLIP interactions: 9 interactions with chain C, Hydrophobic interactions: C:V.39, C:W.41, C:A.42, C:W.75, C:V.92, C:L.257 Hydrogen bonds: C:I.70 Salt bridges: C:H.69 Metal complexes: C:H.96 CLA.36: 19 residues within 4Å: Chain C: W.41, M.45, F.48, Q.62, G.63, L.64, I.65, L.382, S.384, W.403, L.404, S.407, H.408 Chain J: P.17, V.21 Ligands: CLA.34, CLA.42, DGD.49, DGD.50 15 PLIP interactions: 13 interactions with chain C, 1 interactions with chain J, 1 Ligand-Water interactions, Hydrophobic interactions: C:W.41, C:F.48, C:F.48, C:I.65, C:I.65, C:L.382, C:W.403, C:W.403, C:W.403, C:W.403, J:V.21 Hydrogen bonds: C:S.384 pi-Stacking: C:W.403, C:W.403 Metal complexes: H2O.1 CLA.37: 25 residues within 4Å: Chain A: F.23, I.26, L.111, S.114, M.117, G.118, W.121 Chain C: F.242, S.251, Y.252, G.255, S.258, M.259, L.416, H.419, L.420, A.423, R.427 Chain H: V.16, F.19, F.23, D.27 Ligands: CLA.8, CLA.39, BCR.47 19 PLIP interactions: 9 interactions with chain C, 9 interactions with chain A, 1 interactions with chain H, Hydrophobic interactions: C:F.242, C:Y.252, C:Y.252, C:L.420, A:F.23, A:F.23, A:I.26, A:L.111, A:L.111, A:W.121, A:W.121, H:V.16 Hydrogen bonds: C:Y.252, C:R.427 Salt bridges: C:R.427, C:R.427 Metal complexes: C:H.419 pi-Stacking: A:W.121, A:W.121 CLA.38: 18 residues within 4Å: Chain C: L.139, L.143, I.221, C.222, G.225, W.228, H.229, T.232, T.233, P.234, F.235, W.237, A.238, F.242 Chain H: V.20 Ligands: CLA.33, CLA.39, BCR.47 13 PLIP interactions: 12 interactions with chain C, 1 interactions with chain H, Hydrophobic interactions: C:L.139, C:L.143, C:L.143, C:W.228, C:W.237, C:W.237, C:W.237, C:A.238, C:F.242, H:V.20 Hydrogen bonds: C:F.235 Salt bridges: C:H.229 Metal complexes: C:H.229 CLA.39: 24 residues within 4Å: Chain C: M.135, T.136, I.138, L.139, H.142, L.143, L.146, I.221, C.222, W.237, F.242, W.244, Y.249, Y.252, S.253, A.256, L.257, M.260 Ligands: CLA.33, CLA.35, CLA.37, CLA.38, CLA.41, BCR.47 19 PLIP interactions: 18 interactions with chain C, 1 Ligand-Water interactions, Hydrophobic interactions: C:M.135, C:T.136, C:I.138, C:L.139, C:L.139, C:L.146, C:I.221, C:W.237, C:F.242, C:F.242, C:F.242, C:W.244, C:Y.249, C:Y.249, C:Y.252, C:Y.252, C:A.256, C:L.257 Metal complexes: H2O.1 CLA.40: 20 residues within 4Å: Chain C: F.11, W.14, A.15, G.16, N.17, A.18, E.247, L.250, L.254, F.414, F.415, V.417, G.418, W.421, H.422, R.425 Ligands: CLA.41, CLA.42, CLA.43, LHG.59 16 PLIP interactions: 16 interactions with chain C, Hydrophobic interactions: C:W.14, C:A.15, C:N.17, C:A.18, C:L.250, C:L.250, C:F.415, C:F.415, C:V.417, C:W.421, C:W.421 Hydrogen bonds: C:N.17 Salt bridges: C:H.422, C:R.425 pi-Stacking: C:W.421 Metal complexes: C:H.422 CLA.41: 28 residues within 4Å: Chain C: N.17, L.20, I.21, L.27, A.30, H.31, H.34, I.38, Y.127, W.129, M.135, I.138, H.142, L.146, G.246, E.247, Y.249, L.250, S.253, L.254, L.257 Ligands: CLA.34, CLA.35, CLA.39, CLA.40, CLA.42, CLA.43, CLA.44 20 PLIP interactions: 20 interactions with chain C, Hydrophobic interactions: C:N.17, C:L.20, C:L.27, C:L.27, C:A.30, C:H.34, C:W.129, C:W.129, C:W.129, C:I.138, C:H.142, C:L.146, C:L.146, C:Y.249, C:L.250, C:L.250 Hydrogen bonds: C:S.253 Water bridges: C:S.253 pi-Stacking: C:H.34 Metal complexes: C:H.31 CLA.42: 19 residues within 4Å: Chain C: N.17, H.34, L.37, I.38, W.41, L.257, L.411, F.414, F.415 Chain J: P.20, F.23, L.24 Ligands: CLA.34, CLA.35, CLA.36, CLA.40, CLA.41, CLA.43, LHG.59 11 PLIP interactions: 9 interactions with chain C, 2 interactions with chain J, Hydrophobic interactions: C:L.37, C:I.38, C:I.38, C:W.41, C:L.257, C:F.414, C:F.415, J:P.20, J:F.23 Hydrogen bonds: C:N.17 Metal complexes: C:H.34 CLA.43: 37 residues within 4Å: Chain C: T.2, N.3, R.4, W.13, G.16, N.17, R.19, L.20, L.23, K.26, A.30, L.37, G.104, F.105, V.108, A.111, I.112, E.116 Chain J: F.23, L.24, A.27, F.28, W.30, Q.31 Chain Q: I.20, L.23, N.29, L.30 Chain S: M.19, V.20, V.23, P.24, A.28 Ligands: CLA.40, CLA.41, CLA.42, BCR.65 31 PLIP interactions: 5 interactions with chain S, 10 interactions with chain J, 13 interactions with chain C, 3 interactions with chain Q, Hydrophobic interactions: S:V.20, S:V.23, S:P.24, S:P.24, S:A.28, J:F.23, J:L.24, J:A.27, J:F.28, J:W.30, J:W.30, J:W.30, J:Q.31, C:L.20, C:L.20, C:K.26, C:A.30, C:L.37, C:F.105, C:V.108, C:A.111, C:I.112, C:I.112, Q:I.20, Q:L.23, Q:L.30 pi-Stacking: J:W.30, J:W.30 Hydrogen bonds: C:R.19 Salt bridges: C:R.4, C:K.26 CLA.44: 19 residues within 4Å: Chain C: H.31, V.32, A.35, L.103, L.118, F.124, F.125, Y.127, I.138, F.141, H.142, V.145, I.148, G.149 Ligands: CLA.34, CLA.35, CLA.41, CLA.45, BCR.46 11 PLIP interactions: 11 interactions with chain C, Hydrophobic interactions: C:H.31, C:L.118, C:F.124, C:F.125, C:Y.127, C:Y.127, C:I.138, C:I.138, C:F.141, C:I.148 Metal complexes: C:H.142 CLA.45: 13 residues within 4Å: Chain C: L.28, V.32, V.102, L.103, G.106, Y.109, H.110, P.115, L.118, Y.121, F.125 Ligands: CLA.44, BCR.46 15 PLIP interactions: 15 interactions with chain C, Hydrophobic interactions: C:L.28, C:L.28, C:V.32, C:V.32, C:V.102, C:L.103, C:Y.109, C:L.118, C:Y.121, C:F.125, C:F.125, C:F.125 Salt bridges: C:H.110 pi-Stacking: C:F.125 Metal complexes: C:H.110 CLA.52: 29 residues within 4Å: Chain A: M.173, F.196 Chain D: W.37, F.62, L.111, F.135, P.138, V.141, S.144, V.145, F.170, L.171, F.174, Q.175, W.180, T.181, H.186, G.189, V.190, V.193, L.194, L.268, S.271, A.272, V.275 Ligands: CLA.3, CLA.4, CLA.5, PHO.7 19 PLIP interactions: 18 interactions with chain D, 1 interactions with chain A, Hydrophobic interactions: D:W.37, D:F.62, D:L.111, D:L.111, D:F.135, D:P.138, D:V.141, D:F.170, D:L.171, D:F.174, D:Q.175, D:V.190, D:V.193, D:V.193, D:L.194, D:L.268, A:F.196 pi-Stacking: D:W.180 Metal complexes: D:H.186 CLA.53: 20 residues within 4Å: Chain D: I.24, L.25, P.28, C.29, L.32, L.78, L.79, L.80, L.81, W.82, W.93, T.101, F.102, L.105, H.106, F.109 Chain G: L.42 Chain R: V.19, L.20 Ligands: BCR.54 15 PLIP interactions: 12 interactions with chain D, 3 interactions with chain R, Hydrophobic interactions: D:L.25, D:P.28, D:P.28, D:L.32, D:W.82, D:W.82, D:L.105, D:F.109, R:V.19, R:V.19, R:L.20 Hydrogen bonds: D:L.81 Salt bridges: D:H.106 pi-Stacking: D:F.102 Metal complexes: D:H.106

2 x PHO: PHEOPHYTIN A(Non-covalent)

PHO.6: 32 residues within 4Å: Chain A: L.31, A.34, T.35, F.38, I.105, F.109, Y.116, Q.120, A.136, Y.137, A.139, P.140, F.148, M.162, L.164, G.165, I.166, T.169, V.195, P.269, V.270, V.273 Chain D: L.194, A.197, L.198, A.201, I.202, W.242, F.246 Ligands: CLA.3, CLA.4, PL9.55 30 PLIP interactions: 4 interactions with chain D, 26 interactions with chain A Hydrophobic interactions: D:L.194, D:A.201, D:I.202, D:F.246, A:L.31, A:L.31, A:A.34, A:F.38, A:F.38, A:F.38, A:I.105, A:F.109, A:F.109, A:F.109, A:Y.116, A:Y.116, A:A.136, A:Y.137, A:Y.137, A:A.139, A:P.140, A:F.148, A:L.164, A:V.195, A:P.269, A:V.273, A:V.273 Hydrogen bonds: A:Y.116, A:Q.120, A:Y.137 PHO.7: 33 residues within 4Å: Chain A: F.196, A.199, L.200, M.204, F.245, L.248, I.249 Chain D: A.30, A.33, L.34, W.37, I.103, G.107, G.110, L.111, F.114, Q.118, N.131, A.134, F.135, A.137, P.138, F.142, F.162, G.163, V.164, I.167, P.264, V.265, L.268 Ligands: CLA.5, PL9.12, CLA.52 26 PLIP interactions: 25 interactions with chain D, 1 interactions with chain A Hydrophobic interactions: D:A.30, D:A.33, D:L.34, D:W.37, D:W.37, D:W.37, D:W.37, D:I.103, D:L.111, D:F.114, D:F.114, D:A.134, D:F.135, D:A.137, D:P.138, D:F.162, D:F.162, D:V.164, D:I.167, D:P.264, D:V.265, D:L.268, A:F.196 Hydrogen bonds: D:Q.118, D:N.131 pi-Stacking: D:F.135

8 x BCR: BETA-CAROTENE(Non-covalent)

BCR.9: 21 residues within 4Å: Chain A: F.7, W.10, G.24, V.25, I.28, P.29, L.32, A.33, I.36, C.37, I.40, A.41, A.44, A.45, I.86, L.92, W.95, L.96, L.104 Chain H: F.15 Ligands: CLA.8 16 PLIP interactions: 14 interactions with chain A, 2 interactions with chain H Hydrophobic interactions: A:F.7, A:W.10, A:V.25, A:I.28, A:P.29, A:A.33, A:I.36, A:I.40, A:A.44, A:I.86, A:L.92, A:W.95, A:L.96, A:L.104, H:F.15, H:F.15 BCR.29: 14 residues within 4Å: Chain B: A.20, M.24, L.28, F.107, A.110, C.111, W.114 Chain L: L.4, I.7, A.8 Ligands: CLA.19, CLA.25, CLA.26, LMG.32 8 PLIP interactions: 3 interactions with chain L, 5 interactions with chain B Hydrophobic interactions: L:L.4, L:I.7, L:A.8, B:M.24, B:L.28, B:F.107, B:W.114, B:W.114 BCR.31: 11 residues within 4Å: Chain B: L.102, L.105, L.108, A.109, C.111, W.112, Y.116 Ligands: CLA.17, CLA.18, CLA.27, CLA.28 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:L.105, B:L.108, B:A.109 BCR.46: 15 residues within 4Å: Chain C: F.90, V.91, V.94, I.98, S.99, L.103, F.125 Chain J: Y.6 Chain S: V.51, V.54, G.55, N.58, F.59 Ligands: CLA.44, CLA.45 7 PLIP interactions: 6 interactions with chain C, 1 interactions with chain S Hydrophobic interactions: C:F.90, C:V.91, C:V.94, C:I.98, C:L.103, C:F.125, S:F.59 BCR.47: 21 residues within 4Å: Chain C: I.187, F.188, Y.190, L.191, I.202, V.205, D.210, V.211, G.214, H.215, I.218, A.241, F.242, M.259 Chain H: V.20, F.23, L.24 Ligands: CLA.33, CLA.37, CLA.38, CLA.39 14 PLIP interactions: 12 interactions with chain C, 2 interactions with chain H Hydrophobic interactions: C:I.187, C:F.188, C:Y.190, C:Y.190, C:I.202, C:V.205, C:V.205, C:I.218, C:I.218, C:A.241, C:F.242, C:F.242, H:F.23, H:L.24 BCR.54: 18 residues within 4Å: Chain D: Y.31, L.32, G.35, G.36, L.38, T.39, F.90, L.99, F.102 Chain F: L.26, P.29, T.30, F.33, L.34, I.37 Chain I: F.28 Ligands: CLA.53, LMG.60 14 PLIP interactions: 8 interactions with chain D, 5 interactions with chain F, 1 interactions with chain I Hydrophobic interactions: D:Y.31, D:L.32, D:L.38, D:F.90, D:L.99, D:F.102, D:F.102, D:F.102, F:L.26, F:P.29, F:F.33, F:L.34, F:I.37, I:F.28 BCR.64: 25 residues within 4Å: Chain C: F.40 Chain I: A.14, T.15, G.18, M.19 Chain J: L.16, I.19, L.22, F.23, A.25, L.26, F.28, V.29, A.32, F.36 Chain Q: I.12, G.13, G.16, P.17 Chain S: V.13, S.16, F.17, V.20 Ligands: SQD.10, BCR.65 12 PLIP interactions: 9 interactions with chain J, 1 interactions with chain S, 1 interactions with chain C, 1 interactions with chain Q Hydrophobic interactions: J:L.16, J:I.19, J:I.19, J:L.22, J:F.23, J:A.25, J:L.26, J:F.28, J:F.36, S:V.20, C:F.40, Q:I.12 BCR.65: 22 residues within 4Å: Chain C: A.33, G.36, L.37, F.40, L.47, V.94, L.97, I.98, S.100, A.101, G.104, A.111 Chain J: Y.6, F.23, A.27, W.30 Chain S: L.12, V.13, S.16, W.47 Ligands: CLA.43, BCR.64 20 PLIP interactions: 10 interactions with chain C, 8 interactions with chain J, 2 interactions with chain S Hydrophobic interactions: C:A.33, C:L.37, C:F.40, C:F.40, C:L.47, C:V.94, C:V.94, C:I.98, C:A.101, C:A.111, J:Y.6, J:Y.6, J:F.23, J:F.23, J:F.23, J:A.27, J:W.30, J:W.30, S:L.12, S:V.13

2 x SQD: 1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL(Non-covalent)

SQD.10: 21 residues within 4Å: Chain A: L.190, F.255, N.257, S.260, F.263, F.264, A.267, W.268, V.271, G.272, F.275 Chain C: Q.6, A.12, W.13, W.14 Chain D: F.221, R.222 Chain J: F.28, F.36 Ligands: LHG.59, BCR.64 19 PLIP interactions: 12 interactions with chain A, 3 interactions with chain J, 3 interactions with chain C, 1 interactions with chain D Hydrophobic interactions: A:L.190, A:L.190, A:F.255, A:F.263, A:F.264, A:A.267, A:W.268, A:W.268, A:V.271, A:F.275, J:F.28, J:F.36, J:F.36, C:W.13 Hydrogen bonds: A:N.257, A:S.260, C:Q.6, C:Q.6 Salt bridges: D:R.222 SQD.56: 13 residues within 4Å: Chain D: W.10, R.13, R.15 Chain F: P.14, F.16, T.17, V.18, V.21 Chain R: I.30, D.34 Chain T: Q.29, L.33 Ligands: PL9.12 8 PLIP interactions: 1 interactions with chain T, 3 interactions with chain D, 2 interactions with chain R, 2 interactions with chain F Hydrogen bonds: T:Q.29, D:R.13, D:R.13, F:V.18 Salt bridges: D:R.15 Hydrophobic interactions: R:I.30, R:I.30, F:V.18

3 x LMG: 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE(Non-covalent)

LMG.11: 16 residues within 4Å: Chain A: F.83, W.87, E.88, F.107, L.111 Chain C: L.191, L.192, K.193, S.194, P.195, F.196, W.201 Chain H: K.5, Y.9 Ligands: CLA.8, DGD.48 16 PLIP interactions: 5 interactions with chain H, 5 interactions with chain A, 6 interactions with chain C Hydrogen bonds: H:K.5, H:K.5, H:Y.9, H:Y.9 Salt bridges: H:K.5 Hydrophobic interactions: A:F.83, A:F.83, A:F.107, A:F.107, A:L.111, C:P.195, C:F.196, C:F.196, C:W.201, C:W.201, C:W.201 LMG.32: 15 residues within 4Å: Chain B: Y.39, T.326, G.327, P.328, K.331, L.436, F.452 Chain K: F.35 Chain L: N.2, L.4, A.8, L.11, F.12 Ligands: CLA.19, BCR.29 8 PLIP interactions: 3 interactions with chain K, 2 interactions with chain L, 3 interactions with chain B Hydrophobic interactions: K:F.35, K:F.35, K:F.35, L:L.11, L:F.12, B:F.452 Hydrogen bonds: B:Y.39, B:T.326 LMG.60: 15 residues within 4Å: Chain D: Y.56, G.59, C.60, N.61, F.62 Chain F: I.37, M.40, Q.41 Chain I: F.28, G.31, A.32, L.36, G.37 Ligands: DGD.50, BCR.54 5 PLIP interactions: 2 interactions with chain I, 1 interactions with chain D, 2 interactions with chain F Hydrogen bonds: I:F.28, I:L.36, F:M.40, F:Q.41 Hydrophobic interactions: D:F.62

2 x PL9: 2,3-DIMETHYL-5-(3,7,11,15,19,23,27,31,35-NONAMETHYL-2,6,10,14,18,22,26,30,34-HEXATRIACONTANONAENYL-2,5-CYCLOHEXADIENE-1,4-DIONE-2,3-DIMETHYL-5-SOLANESYL-1,4-BENZOQUINONE(Non-covalent)

PL9.12: 29 residues within 4Å: Chain A: F.201, M.204, H.205, L.208, Y.236, I.238, A.241, H.242, F.245, I.249, A.253, S.254, F.255, L.261, F.264 Chain D: V.19, G.23, F.27, P.28, A.30, Y.31, L.34 Chain F: V.18, A.22, T.25, L.26 Chain R: L.27 Ligands: PHO.7, SQD.56 22 PLIP interactions: 15 interactions with chain A, 4 interactions with chain D, 1 interactions with chain R, 2 interactions with chain F Hydrophobic interactions: A:F.201, A:F.201, A:M.204, A:H.205, A:L.208, A:L.208, A:Y.236, A:H.242, A:I.249, A:A.253, A:F.255, A:L.261, A:L.261, A:F.264, D:F.27, D:F.27, D:F.27, D:L.34, R:L.27, F:A.22, F:L.26 Hydrogen bonds: A:F.255 PL9.55: 31 residues within 4Å: Chain A: I.166 Chain D: M.187, M.188, A.191, G.192, G.195, L.198, L.199, I.202, H.203, T.206, Y.233, M.235, A.238, N.239, W.242, F.246, I.248, A.249, F.250, L.256, F.259, F.262, V.263, G.267 Chain K: V.26, L.27, L.30 Ligands: CLA.4, PHO.6, LHG.58 23 PLIP interactions: 19 interactions with chain D, 3 interactions with chain K, 1 interactions with chain A Hydrophobic interactions: D:M.187, D:M.188, D:A.191, D:L.198, D:I.202, D:T.206, D:Y.233, D:W.242, D:F.246, D:F.246, D:F.250, D:F.250, D:L.256, D:F.259, D:F.259, D:F.262, D:V.263, K:V.26, K:L.27, K:L.30, A:I.166 Hydrogen bonds: D:H.203, D:F.250

1 x UNL: UNKNOWN LIGAND

UNL.30: 4 residues within 4Å: Chain B: L.28, W.32 Ligands: CLA.19, CLA.25 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:W.32

4 x DGD: DIGALACTOSYL DIACYL GLYCEROL (DGDG)(Non-covalent)

DGD.48: 23 residues within 4Å: Chain A: L.81, I.153 Chain C: W.167, P.195, F.196, G.197, G.198, G.200, W.201, V.203, S.204, V.205, N.206, F.262, C.266, F.270, N.271, N.272, T.273, D.338, F.339, R.340 Ligands: LMG.11 15 PLIP interactions: 15 interactions with chain C Hydrophobic interactions: C:F.196, C:F.196, C:F.262 Hydrogen bonds: C:P.195, C:G.198, C:W.201, C:N.272, C:N.272, C:T.273, C:T.273, C:T.273, C:D.338, C:R.340, C:R.340 Water bridges: C:D.338 DGD.49: 20 residues within 4Å: Chain A: H.185, F.187, T.282, L.287 Chain C: E.61, Q.62, G.63, L.382, S.384, N.396, F.397, V.398, W.403, T.406, S.407, V.410 Chain I: F.29, Y.33 Ligands: CLA.36, DGD.50 16 PLIP interactions: 4 interactions with chain A, 11 interactions with chain C, 1 interactions with chain I Hydrophobic interactions: A:F.187, A:F.187, A:T.282, A:L.287, C:L.382, C:L.382, C:W.403, C:W.403, C:V.410, I:F.29 Hydrogen bonds: C:S.384, C:N.396, C:N.396, C:V.398, C:V.398, C:W.403 DGD.50: 29 residues within 4Å: Chain A: P.186, Q.189, L.190, A.193, W.268, F.290, F.292, S.295 Chain C: L.382, N.383, V.385, N.393, S.394, N.396 Chain D: N.61, F.62, L.63 Chain I: F.29, A.32, Y.33, G.37, S.38, S.39, L.40 Chain P: Q.60 Ligands: CLA.5, CLA.36, DGD.49, LMG.60 20 PLIP interactions: 3 interactions with chain D, 8 interactions with chain A, 5 interactions with chain I, 4 interactions with chain C Hydrophobic interactions: D:F.62, D:L.63, D:L.63, A:P.186, A:L.190, A:A.193, A:W.268, A:W.268, A:F.290, A:F.290, I:F.29, I:F.29 Hydrogen bonds: A:S.295, I:Y.33, I:G.37, I:S.39, C:N.383, C:N.393, C:N.393, C:N.396 DGD.63: 27 residues within 4Å: Chain B: Y.192, F.249, V.250, G.253, Y.257, Y.272, Q.273, S.276, Y.278, T.451, A.455 Chain D: G.75, H.76, L.78, I.148, L.151, G.152, V.276, A.279, L.280 Chain G: L.45, Y.48, N.49, V.59, S.60, W.61 Ligands: CLA.14 15 PLIP interactions: 5 interactions with chain B, 6 interactions with chain D, 4 interactions with chain G Hydrophobic interactions: B:F.249, B:T.451, B:A.455, D:L.78, D:I.148, D:V.276, D:A.279, D:L.280, G:L.45, G:Y.48 Hydrogen bonds: B:Y.192, B:Y.192, D:H.76, G:N.49, G:V.59

1 x BCT: BICARBONATE ION(Non-functional Binders)

BCT.51: 9 residues within 4Å: Chain A: H.205, V.209, Y.236, H.262 Chain D: H.203, Y.233, K.253, H.257 Ligands: FE2.2 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain D Hydrogen bonds: A:Y.236, D:H.203 Water bridges: A:S.258

4 x LHG: 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE(Non-covalent)

LHG.57: 25 residues within 4Å: Chain A: S.222, N.224 Chain B: W.4, Y.5, R.6, F.463, W.467 Chain D: Y.130, I.133, W.255, F.258, L.261, F.262, V.265, T.266, W.269 Chain K: L.23, I.24 Chain L: L.11, F.12, V.15, P.16 Ligands: CLA.23, CLA.25, LHG.66 18 PLIP interactions: 2 interactions with chain A, 6 interactions with chain B, 6 interactions with chain D, 2 interactions with chain L, 2 interactions with chain K Hydrogen bonds: A:S.222, A:N.224, B:Y.5 Hydrophobic interactions: B:W.4, B:W.4, B:F.463, B:F.463, D:F.258, D:L.261, D:F.262, D:F.262, D:V.265, D:W.269, L:F.12, L:V.15, K:L.23, K:I.24 Salt bridges: B:R.6 LHG.58: 19 residues within 4Å: Chain D: F.246, I.248, A.249, F.250, S.251, N.252, W.255, F.259 Chain K: N.13, T.15, S.16, Y.18, L.19, L.22 Chain N: F.17, A.20, I.21 Ligands: PL9.55, LHG.66 14 PLIP interactions: 4 interactions with chain K, 8 interactions with chain D, 2 interactions with chain N Hydrophobic interactions: K:Y.18, K:L.19, D:F.246, D:I.248, D:I.248, D:F.250, D:F.259, D:F.259, N:A.20, N:I.21 Hydrogen bonds: K:N.13, K:S.16, D:S.251, D:N.252 LHG.59: 24 residues within 4Å: Chain A: R.130, W.132, V.135, A.136, F.263, A.266, A.267, V.270, W.274 Chain C: F.11, W.14, A.15, W.421, R.425 Chain D: A.205, E.208, N.209, A.218, S.219, T.220, F.221 Ligands: SQD.10, CLA.40, CLA.42 18 PLIP interactions: 8 interactions with chain A, 6 interactions with chain D, 4 interactions with chain C Hydrophobic interactions: A:V.135, A:A.136, A:F.263, A:A.266, A:V.270, A:W.274, D:A.205, D:E.208, C:W.14, C:W.14, C:W.421 Salt bridges: A:R.130, A:R.130 Hydrogen bonds: D:N.209, D:A.218, D:S.219, D:T.220, C:R.425 LHG.66: 23 residues within 4Å: Chain A: S.222, N.224, Y.225 Chain B: P.3, W.4, Y.5 Chain D: W.255, F.259, F.262 Chain K: E.11, L.12, N.13, S.16, L.19, G.20, L.22 Chain L: P.16, F.19, L.20 Ligands: CLA.23, CLA.26, LHG.57, LHG.58 19 PLIP interactions: 3 interactions with chain A, 6 interactions with chain K, 4 interactions with chain D, 3 interactions with chain B, 3 interactions with chain L Hydrogen bonds: A:S.222, A:S.222, A:N.224, K:E.11, K:N.13, K:N.13, K:S.16, B:W.4 Hydrophobic interactions: K:L.19, K:L.22, D:W.255, D:F.259, D:F.262, D:F.262, B:W.4, B:W.4, L:P.16, L:L.20, L:L.20

1 x HEM: PROTOPORPHYRIN IX CONTAINING FE(Non-covalent)

HEM.61: 21 residues within 4Å: Chain E: R.8, F.10, I.13, R.18, Y.19, I.22, H.23, T.26, I.27, L.30 Chain F: I.15, F.16, R.19, W.20, V.23, H.24, A.27, V.28, I.31 Chain T: A.14, A.18 24 PLIP interactions: 9 interactions with chain F, 13 interactions with chain E, 2 interactions with chain T, Hydrophobic interactions: F:I.15, F:F.16, F:W.20, F:V.23, F:A.27, F:I.31, E:F.10, E:I.13, E:Y.19, E:I.22, E:T.26, E:I.27, E:I.27, T:A.14, T:A.18 Salt bridges: F:R.19, E:R.8, E:R.18 pi-Stacking: F:W.20, F:W.20, E:Y.19 Hydrogen bonds: E:S.16, E:S.16 Metal complexes: E:H.23

1 x RRX: (3R)-beta,beta-caroten-3-ol(Non-covalent)

RRX.62: 17 residues within 4Å: Chain G: M.30, F.33, M.34, L.36, F.37, V.39, F.40, I.43, L.54 Chain R: T.1, I.2, L.6, F.10 Ligands: CLA.13, CLA.14, CLA.21, CLA.22 12 PLIP interactions: 9 interactions with chain G, 3 interactions with chain R Hydrophobic interactions: G:F.33, G:L.36, G:F.37, G:F.37, G:F.37, G:V.39, G:F.40, G:I.43, G:L.54, R:I.2, R:F.10, R:F.10

1 x HEC: HEME C(Covalent)

HEC.67: 26 residues within 4Å: Chain C: A.371 Chain P: A.62, C.63, S.65, C.66, H.67, T.72, T.74, N.75, L.78, D.79, L.80, T.84, L.85, A.88, L.98, Y.101, M.102, T.107, Y.108, I.114, H.118, P.119, M.130, I.141, I.145 16 PLIP interactions: 15 interactions with chain P, 1 interactions with chain C, Hydrophobic interactions: P:T.72, P:N.75, P:L.78, P:L.80, P:L.98, P:Y.101, P:I.114, P:P.119, P:I.141, P:I.145, C:A.371 Hydrogen bonds: P:N.75, P:Y.108 pi-Stacking: P:Y.101 Metal complexes: P:H.67, P:H.118

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Yu, H. et al., Cryo-EM structure of monomeric photosystem II at 2.78 angstrom resolution reveals factors important for the formation of dimer. Biochim Biophys Acta Bioenerg (2021)

Release Date

2021-07-07

Peptides

Photosystem II protein D1: A
Photosystem II CP47 reaction center protein: B
Photosystem II CP43 reaction center protein: C
Photosystem II D2 protein: D
Cytochrome b559 subunit alpha: E
Cytochrome b559 subunit beta: F
Photosystem II reaction center protein H: G
Photosystem II reaction center protein I: H
Photosystem II reaction center protein J: I
Photosystem II reaction center protein K: J
Photosystem II reaction center protein L: K
Photosystem II reaction center protein M: L
Photosystem II manganese-stabilizing polypeptide: M
Photosystem II reaction center protein T: N
Photosystem II 12 kDa extrinsic protein: O
Cytochrome c-550: P
Photosystem II reaction center protein Ycf12: Q
Photosystem II reaction center protein X: R
Photosystem II reaction center protein Z: S
Photosystem II protein Y: T

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

G
H

H
I

I
J

J
K

K
L

L
M

M
O

N
T

O
U

P
V

Q
Y

R
X

S
Z

T
R

Membrane

We predict this structure to be a membrane protein.
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Photosystem II protein D1

Photosystem II CP47 reaction center protein

Photosystem II CP43 reaction center protein

Photosystem II D2 protein

Cytochrome b559 subunit alpha

Cytochrome b559 subunit beta

Photosystem II reaction center protein H

Photosystem II reaction center protein I

Photosystem II reaction center protein J

Photosystem II reaction center protein K

Photosystem II reaction center protein L

Photosystem II reaction center protein M

Photosystem II manganese-stabilizing polypeptide

Photosystem II reaction center protein T

Photosystem II 12 kDa extrinsic protein

Cytochrome c-550

Photosystem II reaction center protein Ycf12

Photosystem II reaction center protein X

Photosystem II reaction center protein Z

Photosystem II protein Y

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