SMTL ID : 1dxr.1

Photosynthetic reaction center from Rhodopseudomonas viridis - His L168 Phe mutant (terbutryn complex)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.00 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, L.71, M.74, I.77, T.78, S.82, C.87, C.90, H.91, L.96, A.97, Y.104, A.107, R.108 Ligands: HEC.2 22 PLIP interactions: 22 interactions with chain A, Hydrophobic interactions: A:Y.56, A:Y.56, A:V.59, A:F.70, A:F.70, A:L.71, A:M.74, A:I.77, 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, A:H.91 Metal complexes: A:H.91 HEC.2: 24 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, T.307 Ligands: HEC.1, HEC.4 12 PLIP interactions: 12 interactions with chain A, Hydrophobic interactions: A:I.77, A:V.81, A:P.103, A:V.106, A:M.110, A:L.111, A:V.145, A:P.301, A:T.307 Salt bridges: A:R.293, A:R.293 Metal complexes: A:H.136 HEC.3: 25 residues within 4Å: Chain A: V.201, R.202, V.203, V.204, T.229, F.230, M.233, M.234, S.237, L.240, T.242, N.243, C.244, C.247, H.248, F.253, E.254, R.264, A.267, W.268, I.271, R.272 Chain C: Y.162 Chain D: I.189 Ligands: HEC.4 29 PLIP interactions: 27 interactions with chain A, 1 interactions with chain D, 1 interactions with chain C, Hydrophobic interactions: A:V.201, 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, A:W.268, A:I.271, D:I.189, C:Y.162 Hydrogen bonds: A:V.203, A:V.204, A:E.254 Water bridges: A:R.202, A:Q.206, A:R.264, A:R.272, 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: 25 residues within 4Å: Chain A: H.124, V.125, A.126, 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: HEC.2, HEC.3 23 PLIP interactions: 23 interactions with chain A, Hydrophobic interactions: A:V.125, A:V.130, A:I.236, A:Q.263, A:Q.263, A:I.266, A:A.267, A:I.271, A:K.314 Hydrogen bonds: A:T.128, A:T.128, A:Q.263 Water bridges: A:T.313, A:K.314, A:K.314 Salt bridges: A:K.314, A:K.314 pi-Stacking: A:H.124, A:H.124, A:H.309, A:H.309 Metal complexes: A:H.124, A:H.309

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

LDA.5: 5 residues within 4Å: Chain B: L.29, R.33 Chain D: F.256, W.266 Ligands: LDA.20 3 PLIP interactions: 3 interactions with chain D Hydrophobic interactions: D:F.256, D:W.266 pi-Cation interactions: D:F.256 LDA.6: 11 residues within 4Å: Chain B: R.34, 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 B Hydrophobic interactions: B:L.62, B:Y.64, B:P.65, B:R.81 pi-Cation interactions: B:Y.64 LDA.14: 11 residues within 4Å: Chain B: W.17 Chain C: D.60, F.62, L.151 Chain D: Y.195, C.197, W.295, C.296, H.299, G.300, A.301 8 PLIP interactions: 3 interactions with chain C, 2 interactions with chain B, 3 interactions with chain D Hydrophobic interactions: C:L.151, B:W.17, B:W.17, D:W.295, D:H.299, D:A.301 Hydrogen bonds: C:D.60 Salt bridges: C:D.60 LDA.19: 10 residues within 4Å: Chain D: W.23, A.53, S.54, A.57, L.122, G.125, S.126, I.129, S.133 Ligands: SO4.24 3 PLIP interactions: 3 interactions with chain D Hydrophobic interactions: D:A.53, D:A.57, D:I.129 LDA.20: 5 residues within 4Å: Chain C: Y.29 Chain D: I.254, F.256 Ligands: LDA.5, BCB.9 No protein-ligand interaction detected (PLIP) LDA.21: 5 residues within 4Å: Chain D: I.68, F.71, N.72, A.75, W.112 4 PLIP interactions: 4 interactions with chain D Hydrophobic interactions: D:F.71, D:F.71, D:W.112, D:W.112

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

SO4.7: 6 residues within 4Å: Chain B: R.33, R.37, Y.41, L.43, E.61 Chain D: R.251 5 PLIP interactions: 2 interactions with chain D, 3 interactions with chain B Water bridges: D:R.251 Salt bridges: D:R.251, B:R.37 Hydrogen bonds: B:R.33, B:Y.41 SO4.22: 3 residues within 4Å: Chain C: N.199 Chain D: H.143, R.265 5 PLIP interactions: 2 interactions with chain B, 3 interactions with chain D Water bridges: B:K.66, B:K.66, D:R.265 Salt bridges: D:H.143, D:R.265 SO4.23: 3 residues within 4Å: Chain B: L.246 Chain D: A.1, R.226 9 PLIP interactions: 1 interactions with chain B, 7 interactions with chain D, 1 interactions with chain C Water bridges: B:T.211, D:A.1, D:D.2, D:R.226, D:R.226, D:R.226, C:W.115 Hydrogen bonds: D:A.1 Salt bridges: D:R.226 SO4.24: 7 residues within 4Å: Chain D: W.23, Y.50, G.52, A.53, S.54, S.133 Ligands: LDA.19 6 PLIP interactions: 6 interactions with chain D Hydrogen bonds: D:Y.50, D:A.53, D:S.54, D:S.133 Water bridges: D:G.55, D:R.134

4 x BCB: BACTERIOCHLOROPHYLL B(Non-covalent)

BCB.8: 29 residues within 4Å: Chain C: F.97, P.124, M.127, F.128, L.131, V.157, N.158, F.160, G.161, Y.162, W.167, F.168, G.172, H.173, S.176, V.177, L.180, F.181, I.240, F.241, G.244, G.247, T.248 Chain D: Y.195, Y.208 Ligands: BCB.9, BPB.10, BCB.15, BCB.16 21 PLIP interactions: 21 interactions with chain C, Hydrophobic interactions: C:F.97, C:F.97, C:P.124, C:M.127, C:F.160, C:Y.162, C:W.167, C:W.167, C:F.168, C:F.168, C:L.180, C:F.181, C:F.181, C:I.240, C:F.241, C:F.241, C:F.241 Hydrogen bonds: C:S.176, C:T.248 pi-Stacking: C:W.167 Metal complexes: C:H.173 BCB.9: 20 residues within 4Å: Chain C: I.49, F.128, F.146, I.150, H.153, L.154, V.157 Chain D: Y.195, G.201, I.204, G.205, Y.208, G.209, L.212, F.270 Ligands: BCB.8, BPB.10, MQ9.12, BCB.16, LDA.20 12 PLIP interactions: 6 interactions with chain D, 6 interactions with chain C, Hydrophobic interactions: D:Y.195, D:I.204, D:I.204, D:L.212, D:F.270, C:I.49, C:F.146, C:F.146, C:L.154, C:V.157 pi-Stacking: D:Y.208 Metal complexes: C:H.153 BCB.15: 22 residues within 4Å: Chain C: F.168, M.174, V.177, S.178, F.181, V.182, M.185, V.220, Y.222 Chain D: M.120, F.154, V.155, I.158, I.177, W.178, H.180, I.181, L.184 Ligands: BCB.8, BCB.16, BPB.17, NS5.18 14 PLIP interactions: 7 interactions with chain D, 7 interactions with chain C, Hydrophobic interactions: D:F.154, D:V.155, D:I.158, D:I.177, D:I.181, D:L.184, C:F.168, C:V.177, C:F.181, C:V.182, C:V.182, C:Y.222 Metal complexes: D:H.180 pi-Stacking: C:F.181 BCB.16: 30 residues within 4Å: Chain C: V.157, Y.162, F.181 Chain D: G.62, I.66, I.69, M.120, L.124, F.148, A.151, F.154, V.155, I.158, W.183, L.184, F.187, S.188, F.194, Y.195, H.200, S.203, I.204, Y.208, M.275, A.278, I.282 Ligands: BCB.8, BCB.9, BCB.15, BPB.17 18 PLIP interactions: 18 interactions with chain D, Hydrophobic interactions: D:I.69, D:L.124, D:F.148, D:A.151, D:F.154, D:V.155, D:W.183, D:L.184, D:F.187, D:F.194, D:Y.195, D:Y.195, D:I.204, D:Y.208 Hydrogen bonds: D:Y.195, D:S.203 Salt bridges: D:H.200 Metal complexes: D:H.200

2 x BPB: BACTERIOPHEOPHYTIN B(Non-covalent)

BPB.10: 27 residues within 4Å: Chain C: F.41, I.42, I.49, C.92, A.93, F.97, W.100, E.104, V.117, A.120, F.121, P.124, F.146, Y.148, G.149, I.150, H.153, A.237, F.241 Chain D: Y.208, G.211, L.212, W.250, I.254 Ligands: BCB.8, BCB.9, MQ9.12 15 PLIP interactions: 1 interactions with chain D, 14 interactions with chain C Hydrophobic interactions: D:Y.208, C:I.42, C:I.49, C:A.120, C:F.121, C:F.121, C:F.121, C:P.124, C:F.146, C:Y.148, C:Y.148, C:H.153, C:F.241, C:F.241 Hydrogen bonds: C:E.104 BPB.17: 21 residues within 4Å: Chain C: F.181, M.185, L.189, V.220 Chain D: A.58, F.59, G.62, S.63, I.66, S.123, L.124, W.127, V.131, I.144, N.147, F.148, S.271, V.274, M.275 Ligands: BCB.15, BCB.16 8 PLIP interactions: 7 interactions with chain D, 1 interactions with chain C Hydrophobic interactions: D:I.66, D:W.127, D:N.147, D:F.148, D:F.148, D:F.148, D:V.274, C:F.181

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

FE2.11: 5 residues within 4Å: Chain C: H.190, H.230 Chain D: H.217, E.232, H.264 5 PLIP interactions: 2 interactions with chain C, 3 interactions with chain D Metal complexes: C:H.190, C:H.230, D:H.217, D:E.232, D:H.264

1 x MQ9: MENAQUINONE-9(Non-covalent)

MQ9.12: 24 residues within 4Å: Chain C: Y.29, G.35, I.39, I.42, F.43, V.46, W.100 Chain D: 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.9, BPB.10 23 PLIP interactions: 12 interactions with chain C, 11 interactions with chain D Hydrophobic interactions: C:Y.29, C:Y.29, C:Y.29, C:I.39, C:I.39, C:I.42, C:F.43, C:F.43, C:V.46, C:W.100, C:W.100, C:W.100, D:A.216, D:A.246, D:W.250, D:I.254, D:F.256, D:F.256, D:I.260, D:V.263, D:W.266, D:F.270 Hydrogen bonds: D:A.258

1 x MST: 2-T-BUTYLAMINO-4-ETHYLAMINO-6-METHYLTHIO-S-TRIAZINE(Non-covalent)

MST.13: 13 residues within 4Å: Chain C: A.186, L.189, H.190, L.193, E.212, N.213, F.216, Y.222, S.223, I.224, G.225, A.226, I.229 8 PLIP interactions: 8 interactions with chain C Hydrophobic interactions: C:E.212, C:F.216, C:Y.222 Hydrogen bonds: C:Y.222, C:S.223, C:I.224, C:G.225 pi-Stacking: C:F.216

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

NS5.18: 14 residues within 4Å: Chain D: I.66, L.70, F.88, W.113, G.117, T.121, G.159, C.160, W.169, V.173, F.175, G.176, H.180 Ligands: BCB.15 12 PLIP interactions: 12 interactions with chain D Hydrophobic interactions: D:I.66, D:L.70, D:F.88, D:W.113, D:W.169, D:W.169, D:V.173, D:V.173, D:F.175, D:F.175, D:F.175, D:H.180

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Lancaster, C.R. et al., Structural basis of the drastically increased initial electron transfer rate in the reaction center from a Rhodopseudomonas viridis mutant described at 2.00-A resolution. J. Biol. Chem. (2000)

Release Date

2001-01-12

Peptides

PHOTOSYNTHETIC REACTION CENTER CYTOCHROME C SUBUNIT: A
PHOTOSYNTHETIC REACTION CENTER H SUBUNIT: B
PHOTOSYNTHETIC REACTION CENTER L SUBUNIT: C
PHOTOSYNTHETIC REACTION CENTER M SUBUNIT: D

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

B
H

C
L

D
M

Membrane

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

PHOTOSYNTHETIC REACTION CENTER H SUBUNIT

PHOTOSYNTHETIC REACTION CENTER L SUBUNIT

PHOTOSYNTHETIC REACTION CENTER M SUBUNIT

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