SMTL ID : 7sa3.1

Structure of a monomeric photosystem II core complex from a cyanobacterium acclimated to far-red light

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

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

Ligands

1 x CA: CALCIUM ION(Non-covalent)

CA.1: 5 residues within 4Å: Chain A: E.190, E.330, E.334 Chain C: P.403, G.405 5 PLIP interactions: 2 interactions with chain A, 1 interactions with chain C, 2 Ligand-Water interactions Metal complexes: A:E.190, A:E.330, C:G.405, H2O.5, H2O.7

1 x CL: CHLORIDE ION(Non-functional Binders)

CL.2: 3 residues within 4Å: Chain A: N.182 Chain D: K.317, L.321 Ligand excluded by PLIP

28 x CLA: CHLOROPHYLL A(Non-covalent)

CLA.3: 32 residues within 4Å: Chain A: Y.120, L.124, Y.148, P.151, V.152, A.154, T.155, S.157, V.158, F.183, M.184, F.185, F.187, Q.188, I.193, L.194, H.199, G.202, V.203, V.206, L.207, I.284, V.287, A.288, I.291 Chain D: L.182, L.205, F.257 Ligands: CL7.4, CLA.5, PHO.6, CLA.49 21 PLIP interactions: 17 interactions with chain A, 4 interactions with chain D, Hydrophobic interactions: A:L.124, A:L.124, A:Y.148, A:V.152, A:A.154, A:F.183, A:F.185, A:F.187, A:Q.188, A:I.193, A:I.193, A:L.194, A:V.203, A:L.207, A:I.284, D:L.182, D:L.182, D:L.205, D:F.257 pi-Cation interactions: A:H.199 Metal complexes: A:H.199 CLA.5: 17 residues within 4Å: Chain A: M.200, V.203, A.204, G.208, L.211 Chain D: Y.153, T.156, F.157, F.173, V.175, I.178, F.179, F.181, L.182 Ligands: CLA.3, PHO.48, CLA.49 14 PLIP interactions: 10 interactions with chain D, 3 interactions with chain A, 1 Ligand-Water interactions, Hydrophobic interactions: D:Y.153, D:T.156, D:F.157, D:F.157, D:F.173, D:I.178, D:F.179, D:F.181, D:L.182, D:L.182, A:V.203, A:V.203, A:L.211 Metal complexes: H2O.3 CLA.7: 24 residues within 4Å: Chain A: L.37, P.40, L.41, V.44, F.94, Y.95, P.96, I.97, W.98, Q.114, M.115, F.118, H.119 Chain G: L.4, V.8, Y.9, T.11, V.12, S.13, F.15, V.16, G.17 Ligands: BCR.8, CLA.34 22 PLIP interactions: 14 interactions with chain A, 8 interactions with chain G, Hydrophobic interactions: A:L.37, A:P.40, A:L.41, A:L.41, A:V.44, A:F.94, A:P.96, A:I.97, A:W.98, G:L.4, G:V.8, G:V.8, G:Y.9, G:T.11, G:V.12, G:F.15 Hydrogen bonds: A:I.97, G:Y.9 Salt bridges: A:H.119 pi-Stacking: A:H.119, A:H.119 Metal complexes: A:H.119 CLA.11: 16 residues within 4Å: Chain B: E.184, W.185, G.189, F.190, P.192, G.197, V.198, A.200, H.201, A.204, L.205, V.208, I.251, T.255 Ligands: CLA.12, DGD.26 12 PLIP interactions: 12 interactions with chain B, Hydrophobic interactions: B:W.185, B:W.185, B:F.190, B:V.198, B:A.200, B:H.201, B:L.205, B:V.208, B:I.251 pi-Stacking: B:F.190, B:H.201 Metal complexes: B:H.201 CLA.12: 22 residues within 4Å: Chain B: R.68, L.69, A.146, L.149, C.150, F.153, L.158, M.166, V.198, H.201, H.202, L.205, V.244, S.247, G.248, I.251, T.255, T.262 Ligands: CLA.11, F6C.13, CLA.14, CLA.15 14 PLIP interactions: 14 interactions with chain B, Hydrophobic interactions: B:L.69, B:A.146, B:L.149, B:F.153, B:F.153, B:L.205, B:V.244, B:I.251 Hydrogen bonds: B:R.68, B:T.255 Water bridges: B:T.262 Salt bridges: B:R.68 pi-Stacking: B:F.153 Metal complexes: B:H.202 CLA.14: 17 residues within 4Å: Chain B: N.27, C.30, A.31, A.34, L.38, L.62, F.65, V.66, R.68, L.69, H.100, F.103 Ligands: CLA.12, F6C.13, CLA.15, CLA.21, F6C.22 10 PLIP interactions: 10 interactions with chain B, Hydrophobic interactions: B:N.27, B:A.31, B:A.34, B:L.69, B:F.103, B:F.103 Hydrogen bonds: B:R.68 pi-Stacking: B:H.100, B:H.100 Metal complexes: B:H.100 CLA.15: 18 residues within 4Å: Chain B: L.69, G.70, V.71, W.91, V.96, A.99, H.100, I.102, G.152, F.153, F.156, H.157, F.162, G.163, P.164 Ligands: CLA.12, CLA.14, LMT.28 13 PLIP interactions: 13 interactions with chain B, Hydrophobic interactions: B:L.69, B:L.69, B:V.71, B:W.91, B:W.91, B:A.99, B:I.102, B:F.153, B:F.156, B:F.162 pi-Stacking: B:H.157, B:H.157 Metal complexes: B:H.157 CLA.17: 21 residues within 4Å: Chain B: G.236, A.239, S.240, A.243, F.246, S.247, F.463, H.466, I.467, L.471 Chain D: W.32, S.33, L.35, L.36, I.123, M.126, L.127, I.130, E.131 Ligands: CLA.19, CLA.50 11 PLIP interactions: 3 interactions with chain D, 8 interactions with chain B, Hydrophobic interactions: D:L.36, D:I.123, D:I.130, B:F.246, B:F.463, B:F.463, B:I.467, B:L.471 Salt bridges: B:H.466 pi-Stacking: B:H.466 Metal complexes: B:H.466 CLA.18: 9 residues within 4Å: Chain B: F.139, L.143, V.208, I.211, G.212, F.215, H.216, R.220 Ligands: CLA.19 10 PLIP interactions: 10 interactions with chain B, Hydrophobic interactions: B:L.143, B:V.208, B:I.211, B:F.215, B:F.215 Salt bridges: B:H.216, B:R.220 pi-Stacking: B:H.216, B:H.216 Metal complexes: B:H.216 CLA.19: 10 residues within 4Å: Chain B: L.135, F.139, H.142, L.143, T.237, V.244, F.245 Ligands: CLA.17, CLA.18, CLA.21 3 PLIP interactions: 3 interactions with chain B, Hydrophobic interactions: B:L.135, B:L.135 Salt bridges: B:H.142 CLA.20: 15 residues within 4Å: Chain B: R.7, V.8, H.9, T.10, L.238, L.242, L.461, W.462, F.464, G.465, W.468, H.469, R.472 Ligands: CLA.21, F6C.22 15 PLIP interactions: 15 interactions with chain B, Hydrophobic interactions: B:H.9, B:T.10, B:L.242, B:W.462, B:F.464, B:W.468 Hydrogen bonds: B:H.9 Salt bridges: B:R.7, B:H.9, B:R.472 pi-Stacking: B:W.468, B:H.469, B:H.469 pi-Cation interactions: B:R.7 Metal complexes: B:H.469 CLA.21: 21 residues within 4Å: Chain B: H.9, V.12, L.13, L.19, V.22, H.23, H.26, N.27, C.30, I.234, T.237, L.238, G.241, L.242, F.245 Ligands: F6C.13, CLA.14, CLA.19, CLA.20, F6C.22, CLA.23 15 PLIP interactions: 15 interactions with chain B, Hydrophobic interactions: B:V.12, B:L.13, B:L.19, B:V.22, B:H.23, B:H.26, B:I.234, B:I.234, B:T.237, B:L.238, B:L.238 Salt bridges: B:H.23 pi-Stacking: B:H.23, B:H.23 Metal complexes: B:H.23 CLA.23: 12 residues within 4Å: Chain B: L.19, I.20, H.23, I.24, N.27, F.103, V.138, I.141, H.142, L.145 Ligands: CLA.21, CLA.24 8 PLIP interactions: 8 interactions with chain B, Hydrophobic interactions: B:L.19, B:I.20, B:F.103, B:V.138, B:I.141, B:L.145, B:L.145 pi-Stacking: B:H.142 CLA.24: 7 residues within 4Å: Chain B: I.20, I.24, A.110, W.113, H.114, V.120 Ligands: CLA.23 9 PLIP interactions: 9 interactions with chain B, Hydrophobic interactions: B:I.20, B:I.24, B:I.24, B:A.110, B:W.113, B:V.120 pi-Stacking: B:W.113, B:W.113 Metal complexes: B:H.114 CLA.30: 25 residues within 4Å: Chain C: T.100, L.101, L.171, F.174, A.175, F.178, L.188, I.227, I.236, H.240, I.243, L.247, N.281, G.284, Q.285, I.288, F.292, A.299, Y.300 Ligands: CLA.31, CLA.32, CLA.34, F6C.36, BCR.43, DGD.44 17 PLIP interactions: 17 interactions with chain C, Hydrophobic interactions: C:L.171, C:F.174, C:A.175, C:F.178, C:I.227, C:I.243, C:I.243, C:L.247, C:I.288, C:F.292, C:A.299, C:Y.300 pi-Stacking: C:F.178, C:F.178, C:H.240 pi-Cation interactions: C:H.240 Metal complexes: C:H.240 CLA.31: 23 residues within 4Å: Chain C: W.69, I.93, L.94, H.97, L.171, F.174, K.181, V.282, Q.285, A.286, A.289, I.293, Y.300, L.429, H.433, F.436, F.440 Ligands: CLA.30, CLA.32, CLA.33, CLA.38, CLA.39, CLA.41 19 PLIP interactions: 19 interactions with chain C, Hydrophobic interactions: C:W.69, C:I.93, C:L.94, C:L.171, C:K.181, C:V.282, C:Q.285, C:A.286, C:A.289, C:L.429, C:F.436, C:F.436, C:F.440, C:F.440 Hydrogen bonds: C:Y.300 Salt bridges: C:H.97, C:H.433 pi-Stacking: C:H.433 Metal complexes: C:H.433 CLA.32: 21 residues within 4Å: Chain C: A.63, V.66, A.67, W.69, A.70, L.74, L.94, H.97, I.98, L.101, I.120, H.124, L.131, F.174, V.282, Q.285 Ligands: CLA.30, CLA.31, F6C.36, CLA.38, CLA.39 12 PLIP interactions: 12 interactions with chain C, Hydrophobic interactions: C:V.66, C:A.67, C:W.69, C:A.70, C:I.98, C:L.101, C:L.131, C:F.174, C:V.282 Salt bridges: C:H.124 pi-Stacking: C:H.124 Metal complexes: C:H.124 CLA.33: 21 residues within 4Å: Chain C: W.69, M.73, F.76, E.77, Q.90, G.91, I.93, W.428, L.429, A.432, H.433, F.436 Chain H: P.25, I.26, I.29 Chain I: X.18, X.19 Ligands: LMT.10, CLA.31, CLA.39, LMT.45 14 PLIP interactions: 3 interactions with chain H, 10 interactions with chain C, 1 Ligand-Water interactions, Hydrophobic interactions: H:P.25, H:I.26, H:I.29, C:F.76, C:I.93, C:W.428, C:W.428, C:W.428, C:W.428, C:L.429, C:A.432, C:F.436 pi-Stacking: C:W.428 Metal complexes: H2O.6 CLA.34: 24 residues within 4Å: Chain A: F.34, L.37, P.122, L.125, C.126, L.128, G.129, W.132 Chain C: F.267, T.273, S.276, Q.277, G.280, L.441, H.444, L.445, A.448, R.452 Chain G: F.23 Ligands: CLA.7, CLA.30, F6C.36, BCR.43, DGD.44 19 PLIP interactions: 9 interactions with chain A, 1 interactions with chain G, 9 interactions with chain C, Hydrophobic interactions: A:F.34, A:P.122, A:L.125, A:L.125, A:L.128, A:W.132, A:W.132, A:W.132, G:F.23, C:Q.277, C:L.441, C:L.441, C:L.445 pi-Stacking: A:W.132 Hydrogen bonds: C:Q.277, C:R.452 Salt bridges: C:R.452 pi-Cation interactions: C:H.444 Metal complexes: C:H.444 CLA.35: 17 residues within 4Å: Chain C: L.164, I.168, I.246, A.249, G.250, W.253, H.254, V.257, P.258, P.259, L.260, W.262, T.263, L.266 Chain G: I.20 Ligands: F6C.36, BCR.43 13 PLIP interactions: 12 interactions with chain C, 1 interactions with chain G, Hydrophobic interactions: C:L.164, C:I.168, C:I.168, C:I.246, C:W.253, C:W.262, C:T.263, G:I.20 Hydrogen bonds: C:L.260, C:T.263 pi-Stacking: C:H.254 pi-Cation interactions: C:H.254 Metal complexes: C:H.254 CLA.37: 21 residues within 4Å: Chain C: Y.37, W.40, A.41, G.42, N.43, A.44, L.275, L.279, F.439, F.440, V.442, G.443, W.446, H.447, R.450 Chain H: L.32, F.36 Ligands: CLA.38, CLA.39, CLA.40, LHG.53 17 PLIP interactions: 16 interactions with chain C, 1 interactions with chain H, Hydrophobic interactions: C:A.44, C:L.275, C:L.279, C:F.440, C:F.440, C:V.442, C:W.446, H:F.36 Hydrogen bonds: C:N.43, C:N.43, C:A.44 Salt bridges: C:H.447, C:R.450 pi-Stacking: C:W.446, C:H.447, C:H.447 Metal complexes: C:H.447 CLA.38: 24 residues within 4Å: Chain C: N.43, L.46, I.47, F.55, A.58, H.59, H.62, F.152, W.154, V.160, G.271, E.272, Y.274, L.275, S.278, L.279, V.282 Ligands: CLA.31, CLA.32, F6C.36, CLA.37, CLA.39, CLA.40, CLA.41 17 PLIP interactions: 17 interactions with chain C, Hydrophobic interactions: C:N.43, C:L.46, C:F.55, C:F.55, C:F.55, C:A.58, C:H.62, C:F.152, C:W.154, C:W.154, C:W.154, C:V.160, C:Y.274 Hydrogen bonds: C:S.278 pi-Stacking: C:F.55 pi-Cation interactions: C:H.59 Metal complexes: C:H.59 CLA.39: 16 residues within 4Å: Chain C: N.43, H.62, L.65, V.66, W.69, F.439, F.440 Chain H: P.28, I.29, L.32 Ligands: CLA.31, CLA.32, CLA.33, CLA.37, CLA.38, CLA.40 12 PLIP interactions: 4 interactions with chain H, 8 interactions with chain C, Hydrophobic interactions: H:P.28, H:I.29, H:L.32, H:L.32, C:L.65, C:V.66, C:W.69, C:F.439, C:F.440 Hydrogen bonds: C:N.43 pi-Stacking: C:H.62 Metal complexes: C:H.62 CLA.40: 21 residues within 4Å: Chain C: G.29, Y.30, W.39, G.42, N.43, R.45, L.46, L.51, R.54, A.58, H.62, A.139 Chain H: L.32, A.35, F.36, W.38, Q.39 Ligands: CLA.37, CLA.38, CLA.39, BCR.46 11 PLIP interactions: 8 interactions with chain H, 3 interactions with chain C, Hydrophobic interactions: H:L.32, H:A.35, H:F.36, H:W.38, H:Q.39, C:A.58, C:A.139 pi-Stacking: H:W.38, H:W.38, H:W.38 Hydrogen bonds: C:R.45 CLA.41: 15 residues within 4Å: Chain C: L.56, H.59, V.60, A.63, L.131, F.149, F.150, F.152, I.163, F.166, H.167, I.170 Ligands: CLA.31, CLA.38, CLA.42 15 PLIP interactions: 15 interactions with chain C, Hydrophobic interactions: C:L.56, C:H.59, C:F.149, C:F.149, C:F.150, C:F.152, C:I.163, C:I.163, C:F.166, C:F.166, C:F.166, C:F.166, C:I.170 pi-Stacking: C:H.167 Metal complexes: C:H.167 CLA.42: 12 residues within 4Å: Chain C: L.56, V.60, V.130, L.131, G.134, Y.137, H.138, P.143, L.146, Y.147, F.150 Ligands: CLA.41 15 PLIP interactions: 15 interactions with chain C, Hydrophobic interactions: C:L.56, C:L.56, C:V.60, C:V.60, C:V.130, C:L.131, C:L.146, C:F.150, C:F.150 Salt bridges: C:H.138 pi-Stacking: C:Y.137, C:H.138, C:H.138, C:F.150 pi-Cation interactions: C:H.138 CLA.49: 26 residues within 4Å: Chain A: M.184, L.207 Chain D: L.122, P.149, V.152, Y.153, T.156, F.181, L.182, F.185, Q.186, Y.191, T.192, H.197, G.200, V.201, V.204, L.205, L.279, S.282, A.283, M.286 Ligands: CLA.3, CL7.4, CLA.5, PHO.48 18 PLIP interactions: 18 interactions with chain D, Hydrophobic interactions: D:L.122, D:P.149, D:V.152, D:Y.153, D:F.181, D:L.182, D:F.185, D:Q.186, D:T.192, D:V.201, D:V.204, D:V.204, D:L.205, D:L.279 Hydrogen bonds: D:T.156, D:Y.191 pi-Stacking: D:Y.191 Metal complexes: D:H.197 CLA.50: 19 residues within 4Å: Chain D: L.35, L.36, P.39, C.40, L.43, L.89, L.90, L.91, L.92, W.93, W.104, G.109, T.112, F.113, L.116, H.117, F.120 Ligands: CLA.17, BCR.51 17 PLIP interactions: 17 interactions with chain D, Hydrophobic interactions: D:L.36, D:P.39, D:L.43, D:L.91, D:L.92, D:W.93, D:W.93, D:F.113, D:L.116, D:F.120, D:F.120 Hydrogen bonds: D:L.92 Salt bridges: D:H.117 pi-Stacking: D:F.113, D:H.117, D:H.117 Metal complexes: D:H.117

1 x CL7: CHLOROPHYLL D(Non-covalent)

CL7.4: 21 residues within 4Å: Chain A: F.49, V.50, Y.120, T.155, V.158, F.159, L.173, I.177, T.180, F.181, F.183, M.184 Chain D: M.198, V.201, T.202, L.205, L.209 Ligands: CLA.3, PHO.6, CLA.49, PL9.52 11 PLIP interactions: 7 interactions with chain A, 3 interactions with chain D, 1 Ligand-Water interactions, Hydrophobic interactions: A:F.49, A:V.50, A:V.158, A:F.181, A:F.183, D:V.201, D:T.202, D:L.209 Hydrogen bonds: A:Y.120, A:T.155 Metal complexes: H2O.2

2 x PHO: PHEOPHYTIN A(Non-covalent)

PHO.6: 29 residues within 4Å: Chain A: L.42, S.45, I.46, F.49, I.116, Y.120, L.124, Y.127, E.131, A.147, Y.148, A.150, P.151, F.159, M.175, G.176, T.180, V.206, P.280, I.284 Chain D: L.205, A.208, L.209, A.212, I.213, W.253, F.257 Ligands: CLA.3, CL7.4 25 PLIP interactions: 21 interactions with chain A, 4 interactions with chain D Hydrophobic interactions: A:L.42, A:L.42, A:I.46, A:F.49, A:F.49, A:I.116, A:Y.120, A:Y.120, A:L.124, A:A.147, A:Y.148, A:Y.148, A:A.150, A:P.151, A:F.159, A:V.206, A:P.280, A:I.284, D:L.205, D:A.212, D:I.213, D:F.257 Hydrogen bonds: A:Y.127, A:E.131, A:Y.148 PHO.48: 30 residues within 4Å: Chain A: L.207, S.210, L.211, M.215, L.259, I.260 Chain D: L.37, S.41, A.44, I.45, W.48, T.114, G.118, G.121, L.122, F.125, Q.129, N.142, A.145, F.146, P.149, Y.153, F.173, G.174, V.175, P.275, V.276, L.279 Ligands: CLA.5, CLA.49 27 PLIP interactions: 25 interactions with chain D, 2 interactions with chain A Hydrophobic interactions: D:A.44, D:I.45, D:W.48, D:W.48, D:W.48, D:W.48, D:T.114, D:L.122, D:L.122, D:F.125, D:F.125, D:A.145, D:F.146, D:F.146, D:P.149, D:Y.153, D:F.173, D:V.175, D:P.275, D:V.276, D:L.279, D:L.279, A:L.207, A:L.211 Hydrogen bonds: D:Q.129, D:N.142 pi-Stacking: D:F.146

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

BCR.8: 21 residues within 4Å: Chain A: V.36, L.39, P.40, G.43, V.44, T.47, V.48, T.51, A.52, A.55, A.56, I.97, L.103, W.106, L.107, P.112, M.115 Chain G: F.15, L.18 Ligands: CLA.7, LMT.9 15 PLIP interactions: 13 interactions with chain A, 2 interactions with chain G Hydrophobic interactions: A:V.36, A:V.36, A:V.44, A:T.47, A:V.48, A:T.51, A:A.52, A:I.97, A:L.103, A:W.106, A:L.107, A:L.107, A:P.112, G:F.15, G:L.18 BCR.25: 10 residues within 4Å: Chain B: L.29, G.32, F.33, I.101, I.102, G.105, L.106, L.109 Ligands: F6C.16, F6C.22 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:L.29, B:F.33, B:L.109 BCR.43: 18 residues within 4Å: Chain C: I.212, F.213, Y.215, L.216, I.227, V.230, D.235, G.239, H.240, I.243, L.266, F.267, N.281 Chain G: F.23 Ligands: CLA.30, CLA.34, CLA.35, F6C.36 14 PLIP interactions: 13 interactions with chain C, 1 interactions with chain G Hydrophobic interactions: C:I.212, C:F.213, C:Y.215, C:Y.215, C:L.216, C:I.227, C:V.230, C:V.230, C:I.243, C:I.243, C:L.266, C:F.267, C:F.267, G:F.23 BCR.46: 15 residues within 4Å: Chain C: A.61, G.64, L.65, F.118, V.122, L.125, S.128, A.129, G.132 Chain H: F.17, L.20, F.31, A.35, W.38 Ligands: CLA.40 17 PLIP interactions: 9 interactions with chain C, 8 interactions with chain H Hydrophobic interactions: C:A.61, C:L.65, C:L.65, C:F.118, C:V.122, C:V.122, C:L.125, C:L.125, C:A.129, H:F.17, H:F.17, H:L.20, H:F.31, H:F.31, H:F.31, H:A.35, H:W.38 BCR.51: 13 residues within 4Å: Chain D: F.42, L.43, G.46, A.47, F.49, T.50, F.101, W.104, L.110 Chain F: P.28, S.29, F.32 Ligands: CLA.50 10 PLIP interactions: 8 interactions with chain D, 2 interactions with chain F Hydrophobic interactions: D:F.42, D:F.49, D:F.49, D:F.49, D:F.49, D:T.50, D:F.101, D:W.104, F:P.28, F:F.32

6 x LMT: DODECYL-BETA-D-MALTOSIDE(Non-covalent)

LMT.9: 7 residues within 4Å: Chain A: V.50, T.51, A.55, L.73, Y.74 Chain D: R.304 Ligands: BCR.8 5 PLIP interactions: 3 interactions with chain A, 2 interactions with chain D Hydrophobic interactions: A:V.50, A:T.51 Hydrogen bonds: A:L.73, D:R.304, D:R.304 LMT.10: 15 residues within 4Å: Chain A: H.196, F.198, L.298, N.299, G.300 Chain C: N.421, V.423, W.428, S.431, A.432, I.435 Chain I: X.22, X.23 Ligands: CLA.33, LMT.45 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain C Hydrophobic interactions: A:F.198, C:I.435 Hydrogen bonds: A:N.299 LMT.28: 7 residues within 4Å: Chain B: W.75, Q.76, F.90, T.95, I.98, A.99 Ligands: CLA.15 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:W.75, B:F.90, B:F.90, B:F.90, B:T.95, B:A.99 Hydrogen bonds: B:W.75 LMT.29: 7 residues within 4Å: Chain B: A.155, T.159, L.161, Q.179, G.180, A.182, P.183 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:A.155, B:T.159, B:L.161 Hydrogen bonds: B:Q.179, B:G.180 LMT.45: 4 residues within 4Å: Chain C: K.85, W.428 Ligands: LMT.10, CLA.33 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:W.428 Hydrogen bonds: C:K.85 LMT.55: 9 residues within 4Å: Chain B: Y.258 Chain D: G.86, H.87, S.88, L.116, L.158, L.162, W.167 Ligands: DGD.26 5 PLIP interactions: 5 interactions with chain D Hydrophobic interactions: D:L.116, D:L.158, D:W.167, D:W.167 Hydrogen bonds: D:H.87

4 x F6C: Chlorophyll F(Non-covalent)

F6C.13: 20 residues within 4Å: Chain B: F.33, F.61, L.62, F.65, R.68, F.245, G.248, A.249, A.252, M.256, F.451, H.455, F.458, G.459, W.462 Ligands: CLA.12, CLA.14, F6C.16, CLA.21, F6C.22 20 PLIP interactions: 20 interactions with chain B, Hydrophobic interactions: B:F.61, B:F.61, B:L.62, B:F.65, B:F.65, B:F.65, B:F.245, B:A.249, B:A.252, B:F.451, B:F.458, B:F.458, B:W.462, B:W.462 Salt bridges: B:R.68, B:R.68 pi-Stacking: B:F.451, B:F.451 pi-Cation interactions: B:H.455 Metal complexes: B:H.455 F6C.16: 25 residues within 4Å: Chain B: F.33, M.37, F.40, L.44, Q.58, G.59, F.61, L.324, V.327, G.328, R.329, N.447, F.450, F.451, F.453, F.454, H.455, I.457, F.458 Chain D: F.196, I.284 Ligands: F6C.13, F6C.22, BCR.25, LMG.27 20 PLIP interactions: 18 interactions with chain B, 1 interactions with chain D, 1 Ligand-Water interactions, Hydrophobic interactions: B:F.33, B:F.40, B:F.40, B:F.61, B:F.61, B:N.447, B:F.450, B:F.450, B:F.450, B:F.453, B:F.453, B:F.454, B:F.454, B:I.457, B:F.458, D:I.284 Hydrogen bonds: B:G.328 pi-Stacking: B:F.61, B:F.454 Metal complexes: H2O.5 F6C.22: 14 residues within 4Å: Chain B: R.7, H.9, H.26, L.29, C.30, F.33, F.245, W.462 Ligands: F6C.13, CLA.14, F6C.16, CLA.20, CLA.21, BCR.25 10 PLIP interactions: 10 interactions with chain B, Hydrophobic interactions: B:L.29, B:F.33, B:F.33, B:F.245, B:W.462 Salt bridges: B:H.9 pi-Stacking: B:H.26, B:H.26 pi-Cation interactions: B:H.26 Metal complexes: B:H.26 F6C.36: 21 residues within 4Å: Chain C: V.160, A.161, L.164, H.167, I.168, L.171, I.246, L.247, F.267, W.269, Y.274, Q.277, S.278, N.281, Q.285 Ligands: CLA.30, CLA.32, CLA.34, CLA.35, CLA.38, BCR.43 16 PLIP interactions: 15 interactions with chain C, 1 Ligand-Water interactions, Hydrophobic interactions: C:V.160, C:A.161, C:L.164, C:L.164, C:L.171, C:I.246, C:L.247, C:F.267, C:W.269, C:W.269, C:Y.274, C:Q.277, C:N.281 Hydrogen bonds: C:H.167, C:N.281 Metal complexes: H2O.5

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

DGD.26: 14 residues within 4Å: Chain B: A.187, F.190, D.191, P.192, F.250, G.254, Y.258, V.456 Chain D: I.159, L.162, G.163, F.291 Ligands: CLA.11, LMT.55 8 PLIP interactions: 2 interactions with chain D, 6 interactions with chain B Hydrophobic interactions: D:L.162, D:F.291, B:F.190, B:F.190, B:P.192, B:Y.258, B:V.456 Hydrogen bonds: B:F.190 DGD.44: 28 residues within 4Å: Chain A: L.92, F.118, I.121, P.122, L.160, I.164, F.169 Chain C: P.220, T.221, G.222, G.223, E.224, G.225, W.226, V.228, S.229, V.230, N.231, A.291, F.295, N.296, N.297, T.298, D.363, A.364, R.365 Ligands: CLA.30, CLA.34 25 PLIP interactions: 7 interactions with chain A, 18 interactions with chain C Hydrophobic interactions: A:F.118, A:F.118, A:I.121, A:P.122, A:L.160, A:I.164, A:F.169, C:P.220, C:T.221, C:W.226, C:V.228, C:A.291 Hydrogen bonds: C:T.221, C:G.223, C:W.226, C:N.297, C:N.297, C:T.298, C:T.298, C:T.298, C:D.363, C:R.365, C:R.365 Water bridges: C:N.231, C:D.363

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

LMG.27: 4 residues within 4Å: Chain B: R.329, V.436, Y.437 Ligands: F6C.16 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.329 Salt bridges: B:R.329 LMG.54: 12 residues within 4Å: Chain D: W.48, F.49, Y.67, G.70, C.71, N.72, F.73 Chain F: I.36, M.39, Q.40, R.44 Chain I: X.17 11 PLIP interactions: 4 interactions with chain F, 7 interactions with chain D Hydrogen bonds: F:M.39, F:Q.40, F:R.44, F:R.44, D:F.73 Hydrophobic interactions: D:W.48, D:F.49, D:F.49, D:F.73, D:F.73, D:F.73

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

FE2.47: 5 residues within 4Å: Chain A: H.216, H.273 Chain D: H.214, E.241, H.268 5 PLIP interactions: 3 interactions with chain D, 2 interactions with chain A Metal complexes: D:H.214, D:E.241, D:H.268, A:H.216, A:H.273

1 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)

PL9.52: 22 residues within 4Å: Chain A: I.177 Chain D: M.199, T.202, G.203, L.209, L.210, I.213, H.214, T.217, Y.244, M.246, N.250, W.253, F.257, I.259, A.260, F.261, F.270, F.273, V.274, G.278 Ligands: CL7.4 13 PLIP interactions: 1 interactions with chain A, 12 interactions with chain D Hydrophobic interactions: A:I.177, D:M.199, D:L.209, D:L.210, D:T.217, D:Y.244, D:W.253, D:F.257, D:I.259, D:F.273, D:V.274, D:V.274 Hydrogen bonds: D:F.261

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

LHG.53: 24 residues within 4Å: Chain A: R.141, W.143, I.146, A.147, F.274, A.277, A.278, V.282, W.285, F.286 Chain C: Y.37, W.40, W.446, R.450 Chain D: A.216, Q.219, N.220, K.229, N.230, T.231, F.232 Chain I: X.7, X.11 Ligands: CLA.37 20 PLIP interactions: 4 interactions with chain C, 13 interactions with chain A, 3 interactions with chain D Hydrophobic interactions: C:W.40, C:W.40, A:W.143, A:I.146, A:A.147, A:F.274, A:F.274, A:A.277, A:A.278, A:V.282, A:V.282, A:W.285, A:F.286, D:A.216 Hydrogen bonds: C:R.450, C:R.450, D:N.220, D:T.231 Salt bridges: A:R.141, A:R.141

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

HEM.56: 11 residues within 4Å: Chain E: Y.19, H.23, T.26, I.27, L.30 Chain F: R.18, W.19, H.23, A.26, I.27, V.30 9 PLIP interactions: 3 interactions with chain E, 6 interactions with chain F, Hydrophobic interactions: E:I.27, E:I.27, E:L.30, F:A.26, F:I.27, F:V.30 pi-Stacking: F:W.19, F:H.23 Metal complexes: F:H.23

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Gisriel, C.J. et al., Structure of a monomeric photosystem II core complex from a cyanobacterium acclimated to far-red light reveals the functions of chlorophylls d and f. J.Biol.Chem. (2021)

Release Date

2021-12-01

Peptides

Photosystem q(B) protein: 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 I: G
Photosystem II reaction center protein K: H
Unknown: I

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

G
I

H
K

I
N

Membrane

We predict this structure to be a membrane protein.
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Photosystem q(B) protein

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 I

Photosystem II reaction center protein K

Unknown

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