SMTL ID : 4h13.1

Crystal Structure of the Cytochrome b6f Complex from Mastigocladus laminosus with TDS

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 3.07 Å

Oligo State

hetero-2-2-2-2-2-2-2-2-mer

Ligands

2 x CD: CADMIUM ION(Non-covalent)

CD.1: 3 residues within 4Å: Chain A: N.74, E.75 Chain C: H.143 4 PLIP interactions: 1 interactions with chain C, 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: C:H.143, A:E.75, H2O.1, H2O.1 CD.20: 3 residues within 4Å: Chain I: N.74, E.75 Chain K: H.143 4 PLIP interactions: 1 interactions with chain I, 1 interactions with chain K, 2 Ligand-Water interactions Metal complexes: I:E.75, K:H.143, H2O.1, H2O.2

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

HEM.2: 29 residues within 4Å: Chain A: F.44, Q.47, F.48, G.51, F.52, M.54, T.55, Y.58, V.69, I.72, R.83, H.86, R.87, A.90, M.93, T.128, F.131, G.132, G.135, Y.136, L.138, P.139, Y.184, H.187, T.188, P.192, I.195 Chain B: E.78 Chain I: F.189 21 PLIP interactions: 20 interactions with chain A, 1 interactions with chain I, Hydrophobic interactions: A:F.44, A:Q.47, A:Q.47, A:M.54, A:T.55, A:Y.58, A:Y.58, A:F.131, A:F.131, A:F.131, A:F.131, A:F.131, A:L.138, A:Y.184, I:F.189 Salt bridges: A:R.83, A:R.83, A:R.87 pi-Stacking: A:H.187 Metal complexes: A:H.86, A:H.187 HEM.3: 31 residues within 4Å: Chain A: Y.34, G.37, G.38, T.40, L.41, M.93, M.97, H.100, V.101, R.103, V.104, T.107, G.109, F.110, R.114, T.117, W.118, G.121, V.122, L.124, A.125, T.128, I.195, M.199, H.202, F.203, I.206, I.211, S.212 Chain B: L.108 Ligands: HEM.4 24 PLIP interactions: 24 interactions with chain A, Hydrophobic interactions: A:T.40, A:V.101, A:V.104, A:T.117, A:W.118, A:W.118, A:W.118, A:V.122, A:L.124, A:L.124, A:A.125, A:F.203, A:I.206 Hydrogen bonds: A:G.37, A:G.38, A:S.212 Water bridges: A:H.100, A:R.114 Salt bridges: A:H.100, A:R.103, A:R.103, A:R.114 Metal complexes: A:H.100, A:H.202 HEM.4: 26 residues within 4Å: Chain A: K.24, V.26, V.30, N.31, Y.34, C.35, G.38, I.39, L.41, T.42, L.45, F.203, I.206, R.207, G.210, I.211 Chain B: N.25, D.35, V.39, F.40, V.43, I.44 Chain H: V.22, R.26 Ligands: HEM.3, TDS.10 16 PLIP interactions: 8 interactions with chain A, 7 interactions with chain B, 1 Ligand-Water interactions, Hydrophobic interactions: A:V.30, A:Y.34, A:F.203, A:I.206, A:I.211, A:I.211, B:V.39, B:F.40, B:V.43, B:V.43, B:I.44 Hydrogen bonds: A:I.211, B:N.25 Salt bridges: A:R.207 pi-Stacking: B:F.40 Metal complexes: H2O.1 HEM.15: 30 residues within 4Å: Chain C: Y.1, P.2, W.4, A.5, T.8, Y.9, I.20, V.21, C.22, C.25, H.26, Q.60, A.63, L.70, N.71, V.72, G.73, A.74, V.75, P.118, N.154, R.155, G.156, R.157, G.158, Q.159, I.160, Y.161, P.162, S.167 18 PLIP interactions: 18 interactions with chain C, Hydrophobic interactions: C:Y.1, C:Y.1, C:P.2, C:W.4, C:W.4, C:A.5, C:N.71, C:V.75, C:R.157, C:Y.161 Hydrogen bonds: C:N.71, C:N.71, C:N.71, C:R.157, C:Y.161 Salt bridges: C:R.157 pi-Stacking: C:W.4 Metal complexes: C:H.26 HEM.21: 29 residues within 4Å: Chain A: F.189 Chain I: F.44, Q.47, F.48, G.51, F.52, M.54, T.55, Y.58, V.69, I.72, R.83, H.86, R.87, A.90, M.93, T.128, F.131, G.132, G.135, Y.136, L.138, P.139, Y.184, H.187, T.188, P.192, I.195 Chain J: E.78 21 PLIP interactions: 20 interactions with chain I, 1 interactions with chain A, Hydrophobic interactions: I:F.44, I:Q.47, I:Q.47, I:M.54, I:T.55, I:Y.58, I:Y.58, I:F.131, I:F.131, I:F.131, I:F.131, I:F.131, I:L.138, I:Y.184, A:F.189 Salt bridges: I:R.83, I:R.83, I:R.87 pi-Stacking: I:H.187 Metal complexes: I:H.86, I:H.187 HEM.22: 31 residues within 4Å: Chain I: Y.34, G.37, G.38, T.40, L.41, M.93, M.97, H.100, V.101, R.103, V.104, T.107, G.109, F.110, R.114, T.117, W.118, G.121, V.122, L.124, A.125, T.128, I.195, M.199, H.202, F.203, I.206, I.211, S.212 Chain J: L.108 Ligands: HEM.23 24 PLIP interactions: 24 interactions with chain I, Hydrophobic interactions: I:T.40, I:V.101, I:V.104, I:T.117, I:W.118, I:W.118, I:W.118, I:V.122, I:L.124, I:L.124, I:A.125, I:F.203, I:I.206 Hydrogen bonds: I:G.37, I:G.38, I:S.212 Water bridges: I:H.100, I:R.114 Salt bridges: I:H.100, I:R.103, I:R.103, I:R.114 Metal complexes: I:H.100, I:H.202 HEM.23: 26 residues within 4Å: Chain I: K.24, V.26, V.30, N.31, Y.34, C.35, G.38, I.39, L.41, T.42, L.45, F.203, I.206, R.207, G.210, I.211 Chain J: N.25, D.35, V.39, F.40, V.43, I.44 Chain P: V.22, R.26 Ligands: HEM.22, TDS.29 16 PLIP interactions: 7 interactions with chain J, 8 interactions with chain I, 1 Ligand-Water interactions, Hydrophobic interactions: J:V.39, J:F.40, J:V.43, J:V.43, J:I.44, I:V.30, I:Y.34, I:F.203, I:I.206, I:I.211, I:I.211 Hydrogen bonds: J:N.25, I:I.211 pi-Stacking: J:F.40 Salt bridges: I:R.207 Metal complexes: H2O.1 HEM.34: 30 residues within 4Å: Chain K: Y.1, P.2, W.4, A.5, T.8, Y.9, I.20, V.21, C.22, C.25, H.26, Q.60, A.63, L.70, N.71, V.72, G.73, A.74, V.75, P.118, N.154, R.155, G.156, R.157, G.158, Q.159, I.160, Y.161, P.162, S.167 18 PLIP interactions: 18 interactions with chain K, Hydrophobic interactions: K:Y.1, K:Y.1, K:P.2, K:W.4, K:W.4, K:A.5, K:N.71, K:V.75, K:R.157, K:Y.161 Hydrogen bonds: K:N.71, K:N.71, K:N.71, K:R.157, K:Y.161 Salt bridges: K:R.157 pi-Stacking: K:W.4 Metal complexes: K:H.26

4 x OPC: (7R,17E)-4-HYDROXY-N,N,N,7-TETRAMETHYL-7-[(8E)-OCTADEC-8-ENOYLOXY]-10-OXO-3,5,9-TRIOXA-4-PHOSPHAHEPTACOS-17-EN-1-AMINIUM 4-OXIDE(Non-covalent)

OPC.5: 36 residues within 4Å: Chain A: I.39, C.43, M.92, M.96 Chain B: T.47, C.50, I.51, L.54 Chain C: P.37, Q.38, S.39 Chain E: M.1, G.4, A.5, Y.8, I.9 Chain F: E.3, E.4, Y.7, A.8, L.10, L.11, S.12, G.14, L.15, V.18 Chain G: L.5, L.9, L.13 Chain H: V.5, W.8, V.9, L.11, L.12, F.15 Ligands: BCR.19 19 PLIP interactions: 7 interactions with chain H, 7 interactions with chain F, 2 interactions with chain G, 1 interactions with chain C, 1 interactions with chain A, 1 interactions with chain E Hydrophobic interactions: H:W.8, H:W.8, H:L.12, H:F.15, H:F.15, H:F.15, H:F.15, F:Y.7, F:Y.7, F:L.10, F:L.11, F:L.11, F:V.18, G:L.5, G:L.9, A:M.92, E:Y.8 Salt bridges: F:E.3 Hydrogen bonds: C:Q.38 OPC.13: 23 residues within 4Å: Chain A: Y.105, K.111 Chain B: I.87, V.91, L.100, S.103, V.104, G.107, L.108, V.111, I.114, E.115, V.117, N.118, F.120, R.126, P.127, V.128, A.129, I.132, V.139, L.143 Ligands: CLA.12 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:I.87 Hydrogen bonds: B:E.115, B:N.118, B:V.128, B:A.129 OPC.24: 36 residues within 4Å: Chain I: I.39, C.43, M.92, M.96 Chain J: T.47, C.50, I.51, L.54 Chain K: P.37, Q.38, S.39 Chain M: M.1, G.4, A.5, Y.8, I.9 Chain N: E.3, E.4, Y.7, A.8, L.10, L.11, S.12, G.14, L.15, V.18 Chain O: L.5, L.9, L.13 Chain P: V.5, W.8, V.9, L.11, L.12, F.15 Ligands: BCR.38 19 PLIP interactions: 7 interactions with chain N, 2 interactions with chain O, 7 interactions with chain P, 1 interactions with chain I, 1 interactions with chain M, 1 interactions with chain K Hydrophobic interactions: N:Y.7, N:Y.7, N:L.10, N:L.11, N:L.11, N:V.18, O:L.5, O:L.9, P:W.8, P:W.8, P:L.12, P:F.15, P:F.15, P:F.15, P:F.15, I:M.92, M:Y.8 Salt bridges: N:E.3 Hydrogen bonds: K:Q.38 OPC.32: 23 residues within 4Å: Chain I: Y.105, K.111 Chain J: I.87, V.91, L.100, S.103, V.104, G.107, L.108, V.111, I.114, E.115, V.117, N.118, F.120, R.126, P.127, V.128, A.129, I.132, V.139, L.143 Ligands: CLA.31 6 PLIP interactions: 6 interactions with chain J Hydrophobic interactions: J:I.87 Hydrogen bonds: J:E.115, J:E.115, J:N.118, J:V.128, J:A.129

2 x MYS: PENTADECANE(Non-covalent)

MYS.6: 16 residues within 4Å: Chain A: V.126, I.127, V.129, S.130, V.133, T.134, V.151, L.169, R.182, Y.183, A.186, V.190, L.191, L.194 Chain I: F.56 Ligands: TDS.9 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:L.169, A:L.169 MYS.25: 16 residues within 4Å: Chain A: F.56 Chain I: V.126, I.127, V.129, S.130, V.133, T.134, V.151, L.169, R.182, Y.183, A.186, V.190, L.191, L.194 Ligands: TDS.28 2 PLIP interactions: 2 interactions with chain I Hydrophobic interactions: I:L.169, I:L.169

2 x 8K6: Octadecane(Non-covalent)

8K6.7: 15 residues within 4Å: Chain A: L.41, F.44, L.45, F.48, A.49, F.52, A.196, M.199, L.200, F.203 Chain I: F.189, V.190, W.193, L.194, V.197 6 PLIP interactions: 3 interactions with chain I, 3 interactions with chain A Hydrophobic interactions: I:W.193, I:L.194, I:V.197, A:F.48, A:F.48, A:A.196 8K6.26: 15 residues within 4Å: Chain A: F.189, V.190, W.193, L.194, V.197 Chain I: L.41, F.44, L.45, F.48, A.49, F.52, A.196, M.199, L.200, F.203 6 PLIP interactions: 3 interactions with chain A, 3 interactions with chain I Hydrophobic interactions: A:W.193, A:L.194, A:V.197, I:F.48, I:F.48, I:A.196

4 x UMQ: UNDECYL-MALTOSIDE(Non-covalent)

UMQ.8: 8 residues within 4Å: Chain A: N.3, Y.5, D.6, I.14, Q.15, L.17, A.18 Ligands: UMQ.11 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:I.14 Hydrogen bonds: A:N.3, A:N.3, A:Q.15 UMQ.11: 9 residues within 4Å: Chain A: Q.15, A.18, D.19, V.21, T.22 Chain B: W.32 Ligands: UMQ.8, TDS.10, SQD.16 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:Q.15, A:T.22 Hydrophobic interactions: B:W.32 UMQ.27: 8 residues within 4Å: Chain I: N.3, Y.5, D.6, I.14, Q.15, L.17, A.18 Ligands: UMQ.30 4 PLIP interactions: 4 interactions with chain I Hydrophobic interactions: I:I.14 Hydrogen bonds: I:N.3, I:N.3, I:Q.15 UMQ.30: 9 residues within 4Å: Chain I: Q.15, A.18, D.19, V.21, T.22 Chain J: W.32 Ligands: UMQ.27, TDS.29, SQD.35 3 PLIP interactions: 2 interactions with chain I, 1 interactions with chain J Hydrogen bonds: I:Q.15, I:T.22 Hydrophobic interactions: J:W.32

4 x TDS: 8-HYDROXY-5,7-DIMETHOXY-3-METHYL-2-TRIDECYL-4H-CHROMEN-4-ONE(Non-covalent)

TDS.9: 23 residues within 4Å: Chain A: Y.136, V.143, A.147, I.150, V.151, V.154, P.155, I.158, I.165 Chain B: I.75, L.76, P.77, E.78, L.81, V.84, F.85, L.88, M.101 Chain L: L.111, C.128, H.129 Ligands: MYS.6, CLA.12 6 PLIP interactions: 2 interactions with chain B, 3 interactions with chain A, 1 interactions with chain L Hydrophobic interactions: B:L.81, B:L.88, A:I.150, A:I.150, A:P.155 Hydrogen bonds: L:H.129 TDS.10: 17 residues within 4Å: Chain A: V.21, K.24, V.26, R.207 Chain B: N.25, A.31, W.32, D.35, L.36, L.37, F.40, P.41 Chain D: F.24, V.27 Chain H: R.26 Ligands: HEM.4, UMQ.11 6 PLIP interactions: 4 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:L.36, B:L.37, B:F.40, B:P.41 Hydrogen bonds: A:R.207, A:R.207 TDS.28: 23 residues within 4Å: Chain D: L.111, C.128, H.129 Chain I: Y.136, V.143, A.147, I.150, V.151, V.154, P.155, I.158, I.165 Chain J: I.75, L.76, P.77, E.78, L.81, V.84, F.85, L.88, M.101 Ligands: MYS.25, CLA.31 6 PLIP interactions: 3 interactions with chain I, 2 interactions with chain J, 1 interactions with chain D Hydrophobic interactions: I:I.150, I:I.150, I:P.155, J:L.81, J:L.88 Hydrogen bonds: D:H.129 TDS.29: 17 residues within 4Å: Chain I: V.21, K.24, V.26, R.207 Chain J: N.25, A.31, W.32, D.35, L.36, L.37, F.40, P.41 Chain L: F.24, V.27 Chain P: R.26 Ligands: HEM.23, UMQ.30 6 PLIP interactions: 4 interactions with chain J, 2 interactions with chain I Hydrophobic interactions: J:L.36, J:L.37, J:F.40, J:P.41 Hydrogen bonds: I:R.207, I:R.207

2 x CLA: CHLOROPHYLL A(Non-covalent)

CLA.12: 34 residues within 4Å: Chain A: M.97, I.98, V.101, F.102, Y.105, W.118, V.122, I.123, A.125, V.126, V.129 Chain B: W.79, Y.80, L.81, P.83, V.84, I.87, M.101, A.102, V.104, P.105, L.106, L.108, I.109, V.111, I.132, F.133, F.135, G.136, V.139, T.140, L.143 Ligands: TDS.9, OPC.13 16 PLIP interactions: 12 interactions with chain B, 3 interactions with chain A, 1 Ligand-Water interactions, Hydrophobic interactions: B:I.87, B:V.104, B:V.104, B:P.105, B:P.105, B:L.106, B:L.108, B:L.108, B:I.132, B:F.133, B:V.139, A:F.102, A:Y.105, A:Y.105 Hydrogen bonds: B:V.84 Metal complexes: H2O.1 CLA.31: 34 residues within 4Å: Chain I: M.97, I.98, V.101, F.102, Y.105, W.118, V.122, I.123, A.125, V.126, V.129 Chain J: W.79, Y.80, L.81, P.83, V.84, I.87, M.101, A.102, V.104, P.105, L.106, L.108, I.109, V.111, I.132, F.133, F.135, G.136, V.139, T.140, L.143 Ligands: TDS.28, OPC.32 16 PLIP interactions: 12 interactions with chain J, 3 interactions with chain I, 1 Ligand-Water interactions, Hydrophobic interactions: J:I.87, J:V.104, J:V.104, J:P.105, J:P.105, J:L.106, J:L.108, J:L.108, J:I.132, J:F.133, J:V.139, I:F.102, I:Y.105, I:Y.105 Hydrogen bonds: J:V.84 Metal complexes: H2O.2

2 x 7PH: (1R)-2-(dodecanoyloxy)-1-[(phosphonooxy)methyl]ethyl tetradecanoate(Non-covalent)

7PH.14: 17 residues within 4Å: Chain A: F.78, W.80, L.81 Chain B: F.48, V.52, V.56 Chain C: N.253, R.254, W.257, M.258, A.260, F.261, L.264 Chain D: G.33, A.34, Y.36, P.37 13 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B, 5 interactions with chain D, 5 interactions with chain C Hydrophobic interactions: A:F.78, A:W.80, B:F.48, D:A.34, D:Y.36, D:Y.36, D:P.37, C:W.257, C:W.257, C:F.261, C:F.261, C:F.261 Hydrogen bonds: D:Y.36 7PH.33: 17 residues within 4Å: Chain I: F.78, W.80, L.81 Chain J: F.48, V.52, V.56 Chain K: N.253, R.254, W.257, M.258, A.260, F.261, L.264 Chain L: G.33, A.34, Y.36, P.37 13 PLIP interactions: 5 interactions with chain K, 5 interactions with chain L, 2 interactions with chain I, 1 interactions with chain J Hydrophobic interactions: K:W.257, K:W.257, K:F.261, K:F.261, K:F.261, L:A.34, L:Y.36, L:Y.36, L:P.37, I:F.78, I:W.80, J:F.48 Hydrogen bonds: L:Y.36

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

SQD.16: 16 residues within 4Å: Chain B: W.32, P.33, L.37, Y.38 Chain C: L.264, K.275, V.279 Chain D: R.16, N.20, L.21, F.24, G.25, T.26, T.28, G.29 Ligands: UMQ.11 5 PLIP interactions: 1 interactions with chain C, 2 interactions with chain D, 2 interactions with chain B Salt bridges: C:K.275, D:R.16 Hydrogen bonds: D:N.20, B:W.32, B:Y.38 SQD.35: 16 residues within 4Å: Chain J: W.32, P.33, L.37, Y.38 Chain K: L.264, K.275, V.279 Chain L: R.16, N.20, L.21, F.24, G.25, T.26, T.28, G.29 Ligands: UMQ.30 5 PLIP interactions: 2 interactions with chain L, 2 interactions with chain J, 1 interactions with chain K Hydrogen bonds: L:N.20, J:W.32, J:Y.38 Salt bridges: L:R.16, K:K.275

2 x FES: FE2/S2 (INORGANIC) CLUSTER(Non-covalent)

FES.17: 11 residues within 4Å: Chain D: C.108, H.110, L.111, G.112, C.113, C.126, C.128, H.129, G.130, S.131, P.143 4 PLIP interactions: 4 interactions with chain D, Metal complexes: D:C.108, D:H.110, D:C.126, D:H.129 FES.36: 11 residues within 4Å: Chain L: C.108, H.110, L.111, G.112, C.113, C.126, C.128, H.129, G.130, S.131, P.143 4 PLIP interactions: 4 interactions with chain L, Metal complexes: L:C.108, L:H.110, L:C.126, L:H.129

2 x OCT: N-OCTANE(Non-covalent)

OCT.18: 5 residues within 4Å: Chain F: F.17, W.20, G.21, V.24 Ligands: BCR.19 2 PLIP interactions: 2 interactions with chain F Hydrophobic interactions: F:W.20, F:V.24 OCT.37: 5 residues within 4Å: Chain N: F.17, W.20, G.21, V.24 Ligands: BCR.38 2 PLIP interactions: 2 interactions with chain N Hydrophobic interactions: N:W.20, N:V.24

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

BCR.19: 26 residues within 4Å: Chain A: I.32, F.33, C.35, L.36, I.39, M.96, L.99 Chain B: V.43, G.46, T.47, C.50 Chain F: I.16, F.17, W.20 Chain G: L.13, A.16, T.17, G.19, G.20, Y.23 Chain H: F.15, S.18, I.19, V.22 Ligands: OPC.5, OCT.18 10 PLIP interactions: 3 interactions with chain G, 3 interactions with chain A, 3 interactions with chain F, 1 interactions with chain H Hydrophobic interactions: G:L.13, G:Y.23, G:Y.23, A:F.33, A:F.33, A:L.99, F:I.16, F:F.17, F:F.17, H:I.19 BCR.38: 26 residues within 4Å: Chain I: I.32, F.33, C.35, L.36, I.39, M.96, L.99 Chain J: V.43, G.46, T.47, C.50 Chain N: I.16, F.17, W.20 Chain O: L.13, A.16, T.17, G.19, G.20, Y.23 Chain P: F.15, S.18, I.19, V.22 Ligands: OPC.24, OCT.37 10 PLIP interactions: 3 interactions with chain N, 3 interactions with chain O, 1 interactions with chain P, 3 interactions with chain I Hydrophobic interactions: N:I.16, N:F.17, N:F.17, O:L.13, O:Y.23, O:Y.23, P:I.19, I:F.33, I:F.33, I:L.99

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Hasan, S.S. et al., Quinone-dependent proton transfer pathways in the photosynthetic cytochrome b6f complex. Proc.Natl.Acad.Sci.USA (2013)

Release Date

2013-02-13

Peptides

Cytochrome b6: AI
Cytochrome b6-f complex subunit 4: BJ
Apocytochrome f: CK
Cytochrome b6-f complex iron-sulfur subunit: DL
Cytochrome b6-f complex subunit 6: EM
Cytochrome b6-f complex subunit 7: FN
Cytochrome b6-f complex subunit 5: GO
Cytochrome b6-f complex subunit 8: HP

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

I
A

B
B

J
B

C
C

K
C

D
D

L
D

E
E

M
E

F
F

N
F

G
G

O
G

H
H

P
H

Membrane

We predict this structure to be a membrane protein.
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Cytochrome b6

Cytochrome b6-f complex subunit 4

Apocytochrome f

Cytochrome b6-f complex iron-sulfur subunit

Cytochrome b6-f complex subunit 6

Cytochrome b6-f complex subunit 7

Cytochrome b6-f complex subunit 5

Cytochrome b6-f complex subunit 8

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