SMTL ID : 2prc.1

PHOTOSYNTHETIC REACTION CENTER FROM RHODOPSEUDOMONAS VIRIDIS (UBIQUINONE-2 COMPLEX)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.45 Å

Oligo State

hetero-1-1-1-1-mer

Ligands

4 x HEM: PROTOPORPHYRIN IX CONTAINING FE(Covalent)

HEM.1: 23 residues within 4Å: Chain A: Y.56, K.57, N.58, V.59, K.60, V.61, L.62, F.70, L.71, M.74, T.75, I.77, T.78, S.82, C.87, C.90, H.91, L.96, A.97, Y.104, A.107, R.108 Ligands: HEM.2 19 PLIP interactions: 19 interactions with chain A, Hydrophobic interactions: A:Y.56, A:Y.56, A:V.59, A:F.70, A:F.70, A:L.96, A:L.96, A:Y.104, A:A.107, A:R.108 Hydrogen bonds: A:K.57, A:N.58, A:K.60, A:V.61, A:L.62, A:Y.104 Salt bridges: A:R.108 pi-Stacking: A:H.91 Metal complexes: A:H.91 HEM.2: 23 residues within 4Å: Chain A: I.77, V.81, Y.89, Y.102, P.103, V.106, M.110, L.111, M.113, T.114, T.131, C.132, C.135, H.136, P.140, L.141, P.142, V.145, L.289, R.293, P.301 Ligands: HEM.1, HEM.4 10 PLIP interactions: 10 interactions with chain A, Hydrophobic interactions: A:I.77, A:V.106, A:M.110, A:L.111, A:P.142, A:V.145, A:P.301 Salt bridges: A:R.293, A:R.293 Metal complexes: A:H.136 HEM.3: 24 residues within 4Å: Chain A: V.201, R.202, V.203, V.204, T.229, F.230, M.233, M.234, I.236, S.237, T.242, N.243, C.244, C.247, H.248, F.253, E.254, R.264, A.267, W.268, R.272 Chain B: Y.162 Chain C: I.189 Ligands: HEM.4 26 PLIP interactions: 1 interactions with chain C, 24 interactions with chain A, 1 interactions with chain B, Hydrophobic interactions: C:I.189, A:V.201, A:T.229, A:F.230, A:M.233, A:I.236, A:T.242, A:F.253, A:F.253, A:F.253, A:F.253, A:R.264, A:A.267, A:W.268, B:Y.162 Hydrogen bonds: A:V.203, A:V.204, A:E.254 Water bridges: A:V.201, A:R.202, A:R.202 Salt bridges: A:R.202, A:R.272 pi-Stacking: A:H.248, A:H.248 Metal complexes: A:H.248 HEM.4: 24 residues within 4Å: Chain A: H.124, V.125, T.128, G.129, V.130, I.236, L.240, F.246, Q.263, I.266, A.267, G.270, I.271, M.273, V.274, D.304, C.305, C.308, H.309, T.313, K.314, P.315 Ligands: HEM.2, HEM.3 20 PLIP interactions: 20 interactions with chain A, Hydrophobic interactions: A:V.125, A:V.130, A:I.236, A:L.240, A:F.246, A:Q.263, A:Q.263, A:I.266, A:I.266, A:A.267, A:I.271, A:P.315 Hydrogen bonds: A:T.128, A:Q.263 Salt bridges: A:K.314, A:K.314 pi-Stacking: A:H.124, A:H.309 Metal complexes: A:H.124, A:H.309

4 x BCB: BACTERIOCHLOROPHYLL B(Non-covalent)

BCB.5: 30 residues within 4Å: Chain B: F.97, P.124, I.125, M.127, F.128, L.131, V.157, N.158, F.160, G.161, Y.162, W.167, H.168, H.173, S.176, V.177, L.180, F.181, I.240, F.241, G.244, G.247, T.248 Chain C: L.184, Y.195, Y.208 Ligands: BCB.6, BPB.7, BCB.14, BCB.15 15 PLIP interactions: 15 interactions with chain B, Hydrophobic interactions: B:F.97, B:P.124, B:V.157, B:F.160, B:Y.162, B:W.167, B:V.177, B:L.180, B:F.181, B:I.240, B:F.241, B:F.241 Hydrogen bonds: B:T.248 pi-Stacking: B:W.167 Metal complexes: B:H.173 BCB.6: 20 residues within 4Å: Chain B: I.49, F.128, L.131, F.146, I.150, H.153, L.154, V.157 Chain C: Y.195, G.201, I.204, G.205, Y.208, G.209, L.212 Ligands: BCB.5, BPB.7, LDA.9, BCB.15, MQ7.17 13 PLIP interactions: 7 interactions with chain B, 6 interactions with chain C, Hydrophobic interactions: B:I.49, B:F.128, B:L.131, B:F.146, B:L.154, B:V.157, C:Y.195, C:I.204, C:I.204, C:L.212 Metal complexes: B:H.153 Water bridges: C:H.200 pi-Stacking: C:Y.208 BCB.14: 23 residues within 4Å: Chain B: H.168, M.174, V.177, S.178, F.181, V.182, M.185, V.220 Chain C: M.120, F.154, V.155, I.158, V.173, I.177, W.178, H.180, I.181, L.184 Ligands: BCB.5, UQ2.8, BCB.15, BPB.16, NS5.18 12 PLIP interactions: 8 interactions with chain C, 4 interactions with chain B, Hydrophobic interactions: C:F.154, C:V.155, C:I.158, C:V.173, C:I.177, C:I.181, C:L.184, B:V.177, B:F.181, B:V.182 Metal complexes: C:H.180 pi-Stacking: B:F.181 BCB.15: 32 residues within 4Å: Chain B: V.157, Y.162, F.181 Chain C: G.62, A.65, I.66, M.120, L.124, F.148, A.151, I.152, F.154, V.155, I.158, W.183, L.184, T.185, F.187, S.188, F.194, Y.195, H.200, S.203, I.204, Y.208, M.275, A.278, I.282 Ligands: BCB.5, BCB.6, BCB.14, BPB.16 21 PLIP interactions: 21 interactions with chain C, Hydrophobic interactions: C:A.65, C:I.66, C:L.124, C:F.148, C:A.151, C:I.152, C:F.154, C:V.155, C:W.183, C:L.184, C:F.187, C:F.194, C:Y.195, C:Y.195, C:I.204, C:I.204, C:Y.208 Hydrogen bonds: C:Y.195, C:S.203 Salt bridges: C:H.200 Metal complexes: C:H.200

2 x BPB: BACTERIOPHEOPHYTIN B(Non-covalent)

BPB.7: 25 residues within 4Å: Chain B: F.41, I.42, G.45, I.49, F.97, W.100, E.104, V.117, A.120, F.121, P.124, F.128, Y.148, G.149, H.153, A.237, F.241 Chain C: Y.208, G.211, L.212, W.250, I.254 Ligands: BCB.5, BCB.6, MQ7.17 12 PLIP interactions: 10 interactions with chain B, 2 interactions with chain C Hydrophobic interactions: B:I.42, B:I.49, B:A.120, B:F.121, B:F.121, B:F.121, B:F.128, B:Y.148, B:Y.148, B:F.241, C:Y.208, C:L.212 BPB.16: 23 residues within 4Å: Chain B: F.181, M.185, L.189, V.219, V.220 Chain C: A.58, F.59, G.62, S.63, I.66, L.67, S.123, L.124, W.127, V.131, I.144, N.147, F.148, S.271, M.275 Ligands: BCB.14, BCB.15, NS5.18 10 PLIP interactions: 8 interactions with chain C, 2 interactions with chain B Hydrophobic interactions: C:F.59, C:F.59, C:I.66, C:L.67, C:W.127, C:N.147, C:F.148, C:F.148, B:F.181, B:L.189

1 x UQ2: UBIQUINONE-2(Non-covalent)

UQ2.8: 15 residues within 4Å: Chain B: V.182, L.189, H.190, L.193, E.212, N.213, F.216, V.220, Y.222, S.223, I.224, G.225, A.226, I.229 Ligands: BCB.14 13 PLIP interactions: 13 interactions with chain B Hydrophobic interactions: B:V.182, B:L.189, B:L.189, B:F.216, B:F.216, B:F.216, B:V.220, B:I.224, B:I.229, B:I.229 Hydrogen bonds: B:I.224, B:G.225 Water bridges: B:A.226

6 x LDA: LAURYL DIMETHYLAMINE-N-OXIDE(Non-covalent)

LDA.9: 6 residues within 4Å: Chain B: Y.29 Chain C: I.254, G.255, F.256 Ligands: BCB.6, LDA.19 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:F.256 LDA.19: 6 residues within 4Å: Chain C: F.206, F.256, W.266 Chain D: L.29, R.33 Ligands: LDA.9 4 PLIP interactions: 4 interactions with chain C Hydrophobic interactions: C:F.206, C:F.256, C:W.266 pi-Cation interactions: C:F.256 LDA.20: 10 residues within 4Å: Chain B: D.60, F.62, L.151 Chain C: Y.195, C.296, H.299, G.300, A.301 Chain D: W.17, Y.18 6 PLIP interactions: 1 interactions with chain C, 2 interactions with chain D, 3 interactions with chain B Hydrophobic interactions: C:H.299, D:W.17, D:W.17, B:L.151 Hydrogen bonds: B:D.60 Salt bridges: B:D.60 LDA.21: 7 residues within 4Å: Chain C: W.23, A.53, S.54, A.57, S.126, S.133 Ligands: SO4.13 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:A.53, C:A.57 LDA.22: 6 residues within 4Å: Chain C: L.67, F.71, N.72, A.75, H.108, W.112 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:L.67 LDA.24: 10 residues within 4Å: Chain D: P.42, V.59, Y.60, L.62, P.63, Y.64, P.65, P.79, R.80, R.81 5 PLIP interactions: 5 interactions with chain D Hydrophobic interactions: D:Y.64, D:Y.64, D:P.65, D:R.81 pi-Cation interactions: D:Y.64

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

FE2.10: 5 residues within 4Å: Chain B: H.190, H.230 Chain C: H.217, E.232, H.264 5 PLIP interactions: 3 interactions with chain C, 2 interactions with chain B Metal complexes: C:H.217, C:E.232, C:H.264, B:H.190, B:H.230

4 x SO4: SULFATE ION(Non-functional Binders)

SO4.11: 3 residues within 4Å: Chain B: N.199 Chain C: H.143, R.265 3 PLIP interactions: 2 interactions with chain C, 1 interactions with chain D Salt bridges: C:H.143, C:R.265 Water bridges: D:K.66 SO4.12: 3 residues within 4Å: Chain C: A.1, R.226 Chain D: L.246 6 PLIP interactions: 6 interactions with chain C Hydrogen bonds: C:A.1, C:A.1 Water bridges: C:D.2, C:R.226, C:R.226 Salt bridges: C:R.226 SO4.13: 7 residues within 4Å: Chain C: W.23, Y.50, G.52, A.53, S.54, S.133 Ligands: LDA.21 6 PLIP interactions: 6 interactions with chain C Hydrogen bonds: C:Y.50, C:A.53, C:S.54 Water bridges: C:G.55, C:R.134, C:R.134 SO4.23: 5 residues within 4Å: Chain C: R.251, F.256 Chain D: R.33, R.37, Y.41 6 PLIP interactions: 1 interactions with chain C, 5 interactions with chain D Salt bridges: C:R.251, D:R.33, D:R.37 Water bridges: D:R.37, D:Y.41, D:Y.41

1 x MQ7: MENAQUINONE-7(Non-covalent)

MQ7.17: 26 residues within 4Å: Chain B: V.26, Y.29, V.31, G.35, I.39, I.42, W.100, R.103 Chain C: L.212, A.216, H.217, T.220, A.246, A.247, W.250, I.254, F.256, N.257, A.258, T.259, I.260, V.263, W.266, F.270 Ligands: BCB.6, BPB.7 28 PLIP interactions: 16 interactions with chain C, 12 interactions with chain B Hydrophobic interactions: C:L.212, C:A.216, C:T.220, C:A.246, C:W.250, C:W.250, C:W.250, C:F.256, C:F.256, C:I.260, C:V.263, C:V.263, C:W.266, C:F.270, B:V.26, B:Y.29, B:Y.29, B:Y.29, B:Y.29, B:V.31, B:I.39, B:I.39, B:I.42, B:W.100, B:W.100, B:W.100 Hydrogen bonds: C:H.217, C:A.258

1 x NS5: 15-cis-1,2-dihydroneurosporene(Non-covalent)

NS5.18: 17 residues within 4Å: Chain C: F.88, W.113, L.114, G.117, L.118, T.121, G.159, C.160, W.169, V.173, P.174, F.175, G.176, I.177, H.180 Ligands: BCB.14, BPB.16 11 PLIP interactions: 11 interactions with chain C Hydrophobic interactions: C:F.88, C:W.113, C:L.114, C:W.169, C:V.173, C:V.173, C:F.175, C:F.175, C:F.175, C:I.177, C:H.180

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Lancaster, C.R. et al., The coupling of light-induced electron transfer and proton uptake as derived from crystal structures of reaction centres from Rhodopseudomonas viridis modified at the binding site of the secondary quinone, QB. Structure (1997)

Release Date

1998-11-11

Peptides

PHOTOSYNTHETIC REACTION CENTER: A
PHOTOSYNTHETIC REACTION CENTER: B
PHOTOSYNTHETIC REACTION CENTER: C
PHOTOSYNTHETIC REACTION CENTER: D

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

B
L

C
M

D
H

Membrane

We predict this structure to be a membrane protein.
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PHOTOSYNTHETIC REACTION CENTER

PHOTOSYNTHETIC REACTION CENTER

PHOTOSYNTHETIC REACTION CENTER

PHOTOSYNTHETIC REACTION CENTER

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