SMTL ID : 1prc.1 (1 other biounit)

CRYSTALLOGRAPHIC REFINEMENT AT 2.3 ANGSTROMS RESOLUTION AND REFINED MODEL OF THE PHOTOSYNTHETIC REACTION CENTER FROM RHODOPSEUDOMONAS VIRIDIS

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

hetero-1-1-1-1-mer

Ligands

4 x HEC: HEME C(Covalent)

HEC.1: 22 residues within 4Å: Chain A: Y.56, K.57, N.58, V.59, K.60, V.61, L.62, F.70, M.74, I.77, T.78, S.82, G.86, C.87, C.90, H.91, L.96, A.97, Y.104, A.107, R.108 Ligands: HEC.2 19 PLIP interactions: 19 interactions with chain A, Hydrophobic interactions: A:Y.56, A:Y.56, A:V.59, A:F.70, A:I.77, A:L.96, A:L.96, A:Y.104, A:A.107, A:R.108 Hydrogen bonds: A:K.57, A:N.58, A:N.58, A:K.60, A:V.61, A:L.62 Salt bridges: A:R.108 pi-Stacking: A:F.70 Metal complexes: A:H.91 HEC.2: 25 residues within 4Å: Chain A: I.77, V.81, Y.89, Y.102, P.103, V.106, A.107, 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.282, L.289, R.293, P.301 Ligands: HEC.1, HEC.4 13 PLIP interactions: 13 interactions with chain A, Hydrophobic interactions: A:I.77, A:V.81, A:V.106, A:M.110, A:L.111, A:L.141, A:P.142, A:V.145, A:L.282, A:P.301 Salt bridges: A:R.293, A:R.293 Metal complexes: A:H.136 HEC.3: 22 residues within 4Å: Chain A: V.201, R.202, V.203, V.204, T.229, F.230, M.233, S.237, L.240, T.242, N.243, C.244, C.247, H.248, F.253, E.254, R.264, A.267, W.268, R.272 Chain C: I.189 Ligands: HEC.4 25 PLIP interactions: 24 interactions with chain A, 1 interactions with chain C, Hydrophobic interactions: A:V.201, A:R.202, A:T.229, A:F.230, A:M.233, A:L.240, A:T.242, A:F.253, A:F.253, A:F.253, A:F.253, A:R.264, A:A.267, C:I.189 Hydrogen bonds: A:R.202, A:V.203, A:V.204 Water bridges: A:V.201, A:Q.206, A:R.272, A:R.272 Salt bridges: A:R.202, A:R.272 pi-Cation interactions: A:R.264 Metal complexes: A:H.248 HEC.4: 23 residues within 4Å: Chain A: H.124, V.125, T.128, G.129, V.130, I.236, L.240, 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: HEC.2, HEC.3 20 PLIP interactions: 20 interactions with chain A, Hydrophobic interactions: A:V.125, A:V.125, A:V.130, A:I.236, A:L.240, A:Q.263, A:Q.263, A:I.266, A:I.271, A:V.274, 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, A:H.309 Metal complexes: A:H.124, A:H.309

4 x BCB: BACTERIOCHLOROPHYLL B(Non-covalent)(Covalent)

BCB.5: 28 residues within 4Å: Chain B: F.97, F.121, P.124, I.125, M.127, F.128, V.157, 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, T.248 Chain C: Y.195, Y.208 Ligands: BCB.6, BPB.7, BCB.14, BCB.15, MQ7.17 22 PLIP interactions: 22 interactions with chain B, Hydrophobic interactions: B:F.97, B:F.97, B:F.121, B:P.124, B:V.157, B:F.160, B:Y.162, B:W.167, B:W.167, B:V.177, B:L.180, B:F.181, B:I.240, B:F.241, B:F.241, B:F.241 Hydrogen bonds: B:S.176, B:T.248 pi-Stacking: B:W.167, B:H.168 pi-Cation interactions: B:H.173 Metal complexes: B:H.173 BCB.6: 19 residues within 4Å: Chain B: I.49, F.128, 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, BCB.15, MQ7.17, LDA.23 11 PLIP interactions: 6 interactions with chain B, 5 interactions with chain C, Hydrophobic interactions: B:I.49, B:F.128, 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 pi-Stacking: C:Y.208 BCB.14: 21 residues within 4Å: Chain B: H.168, M.174, V.177, S.178, F.181, V.182, M.185, V.220 Chain C: I.49, M.120, F.154, V.155, I.177, W.178, H.180, I.181, L.184 Ligands: BCB.5, BCB.15, BPB.16, NS1.18 12 PLIP interactions: 8 interactions with chain C, 4 interactions with chain B, Hydrophobic interactions: C:I.49, C:F.154, C:V.155, C:I.177, C:I.181, C:L.184, C:L.184, B:V.177, B:F.181, B:V.182 Metal complexes: C:H.180 pi-Stacking: B:F.181 BCB.15: 28 residues within 4Å: Chain B: Y.162, F.181 Chain C: I.69, M.120, L.124, F.148, A.151, F.154, V.155, W.183, L.184, T.185, F.187, S.188, F.194, Y.195, H.200, S.203, I.204, A.207, Y.208, M.275, A.278, I.282 Ligands: BCB.5, BCB.6, BCB.14, BPB.16 24 PLIP interactions: 1 interactions with chain B, 23 interactions with chain C, pi-Cation interactions: B:H.168 Hydrophobic interactions: C:I.69, C:L.124, C:F.148, C:A.151, C:F.154, C:F.154, 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:A.207, C:Y.208 Hydrogen bonds: C:Y.195, C:S.203 Salt bridges: C:H.200 pi-Stacking: C:Y.195 Metal complexes: C:H.200

2 x BPB: BACTERIOPHEOPHYTIN B(Non-covalent)

BPB.7: 25 residues within 4Å: Chain B: I.49, A.93, A.96, F.97, W.100, E.104, V.117, A.120, F.121, V.123, P.124, Y.148, G.149, H.153, A.237, S.238, F.241 Chain C: Y.208, G.211, L.212, A.216, W.250, I.254 Ligands: BCB.5, BCB.6 12 PLIP interactions: 11 interactions with chain B, 1 interactions with chain C Hydrophobic interactions: B:I.49, B:A.96, B:A.120, B:F.121, B:F.121, B:V.123, B:P.124, B:Y.148, B:Y.148, B:F.241, C:Y.208 Hydrogen bonds: B:E.104 BPB.16: 20 residues within 4Å: Chain B: F.181, M.185, L.189, V.220 Chain C: F.59, G.62, S.63, I.66, S.123, L.124, W.127, V.131, I.144, N.147, F.148, S.271, M.275 Ligands: BCB.14, BCB.15, NS1.18 9 PLIP interactions: 2 interactions with chain B, 7 interactions with chain C Hydrophobic interactions: B:F.181, B:L.189, C:F.59, C:I.66, C:N.147, C:F.148, C:F.148, C:F.148, C:F.148

1 x UQ1: UBIQUINONE-1(Non-covalent)

UQ1.8: 13 residues within 4Å: Chain B: L.189, H.190, L.193, I.194, E.212, N.213, F.216, Y.222, S.223, I.224, G.225, A.226, I.229 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:L.189, B:F.216, B:F.216, B:I.224 Hydrogen bonds: B:I.224, B:G.225

1 x FE: FE (III) ION(Non-covalent)

FE.9: 5 residues within 4Å: Chain B: H.190, H.230 Chain C: H.217, E.232, H.264 5 PLIP interactions: 2 interactions with chain B, 3 interactions with chain C Metal complexes: B:H.190, B:H.230, C:H.217, C:E.232, C:H.264

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

SO4.10: 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 SO4.11: 4 residues within 4Å: Chain C: A.1, R.226 Chain D: T.211, L.246 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:A.1, C:A.1 Water bridges: C:D.2, C:R.226 Salt bridges: C:R.226 SO4.12: 7 residues within 4Å: Chain C: W.23, Y.50, L.51, G.52, A.53, S.54, S.133 7 PLIP interactions: 7 interactions with chain C Hydrogen bonds: C:Y.50, C:A.53, C:S.54, C:S.54, C:S.133 Water bridges: C:Y.50, C:G.55 SO4.13: 3 residues within 4Å: Chain C: S.35, Y.36, W.37 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:Y.36, C:W.37 SO4.20: 4 residues within 4Å: Chain C: R.251 Chain D: R.33, R.37, Y.41 5 PLIP interactions: 4 interactions with chain D, 1 interactions with chain C Hydrogen bonds: D:R.33, D:Y.41 Water bridges: D:Y.41 Salt bridges: D:R.37, C:R.251 SO4.21: 3 residues within 4Å: Chain D: Y.117, R.233, K.237 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:Y.117 Salt bridges: D:R.233, D:K.237 SO4.22: 1 residues within 4Å: Chain D: R.34 1 PLIP interactions: 1 interactions with chain D Salt bridges: D:R.34

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

MQ7.17: 20 residues within 4Å: Chain B: V.26, Y.29, V.31, W.100, R.103 Chain C: A.216, H.217, T.220, W.250, I.254, F.256, N.257, A.258, T.259, I.260, V.263, W.266, F.270 Ligands: BCB.5, BCB.6 19 PLIP interactions: 13 interactions with chain C, 6 interactions with chain B Hydrophobic interactions: C:A.216, C:T.220, C:W.250, C:W.250, C:F.256, C:F.256, C:I.260, C:V.263, C:W.266, C:W.266, C:F.270, B:Y.29, B:Y.29, B:Y.29, B:V.31, B:W.100, B:W.100 Hydrogen bonds: C:H.217, C:A.258

1 x NS1: 15-trans-1,2-dihydroneurosporene(Non-covalent)

NS1.18: 18 residues within 4Å: Chain C: I.66, L.70, M.73, F.88, G.117, L.118, T.121, V.155, G.159, C.160, V.173, P.174, F.175, G.176, I.177, H.180 Ligands: BCB.14, BPB.16 12 PLIP interactions: 12 interactions with chain C Hydrophobic interactions: C:I.66, C:I.66, C:L.70, C:L.70, C:F.88, C:L.118, C:V.155, C:V.173, C:V.173, C:F.175, C:I.177, C:H.180

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

LDA.19: 5 residues within 4Å: Chain C: F.202, G.205, F.206, F.256 Chain D: R.33 4 PLIP interactions: 3 interactions with chain C, 1 interactions with chain D Hydrophobic interactions: C:F.206, C:F.256 pi-Cation interactions: C:F.256 Hydrogen bonds: D:R.33 LDA.23: 11 residues within 4Å: Chain B: L.151 Chain C: Y.195, C.197, P.198, G.201, W.295, H.299 Chain D: Q.14, W.17, Y.18 Ligands: BCB.6 6 PLIP interactions: 1 interactions with chain B, 3 interactions with chain C, 2 interactions with chain D Hydrophobic interactions: B:L.151, C:P.198, C:P.198, C:W.295, D:W.17, D:W.17

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Deisenhofer, J. et al., Crystallographic refinement at 2.3 A resolution and refined model of the photosynthetic reaction centre from Rhodopseudomonas viridis. J.Mol.Biol. (1995)

Release Date

1989-01-09

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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