SMTL ID : 1eys.1

CRYSTAL STRUCTURE OF PHOTOSYNTHETIC REACTION CENTER FROM A THERMOPHILIC BACTERIUM, THERMOCHROMATIUM TEPIDUM

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

hetero-1-1-1-1-mer

Ligands

4 x HEM: PROTOPORPHYRIN IX CONTAINING FE(Covalent)

HEM.1: 21 residues within 4Å: Chain A: Y.54, Q.55, S.56, V.57, Q.58, V.59, L.60, F.68, M.72, V.75, T.76, C.85, C.88, H.89, W.94, A.95, K.102, S.105, R.106, F.109 Ligands: HEM.2 16 PLIP interactions: 16 interactions with chain A, Hydrophobic interactions: A:Y.54, A:Y.54, A:F.68, A:M.72, A:V.75, A:T.76, A:R.106, A:F.109 Hydrogen bonds: A:Q.55, A:S.56, A:S.56, A:Q.58, A:V.59, A:L.60 Salt bridges: A:R.106 Metal complexes: A:H.89 HEM.2: 23 residues within 4Å: Chain A: V.75, V.79, Y.87, Y.100, T.101, V.104, S.105, M.108, V.112, T.129, C.130, C.133, H.134, P.138, V.139, P.140, A.143, L.269, R.273, L.281, R.282, V.283 Ligands: HEM.1 12 PLIP interactions: 12 interactions with chain A, Hydrophobic interactions: A:V.75, A:V.79, A:V.104, A:M.108, A:V.112, A:P.140, A:A.143, A:L.281, A:V.283 Salt bridges: A:R.273, A:R.273 Metal complexes: A:H.134 HEM.3: 24 residues within 4Å: Chain A: I.188, R.189, I.190, T.191, T.210, F.211, M.214, I.217, S.218, L.221, V.223, G.224, C.225, C.228, H.229, F.234, N.235, R.244, A.247, W.248, R.252 Chain B: L.173 Chain C: I.190, Y.316 19 PLIP interactions: 17 interactions with chain A, 2 interactions with chain C, Hydrophobic interactions: A:I.190, A:T.210, A:F.211, A:M.214, A:I.217, A:L.221, A:V.223, A:F.234, A:F.234, A:R.244, A:A.247, C:I.190 Hydrogen bonds: A:I.190, A:T.191, C:Y.316 Water bridges: A:N.235, A:R.244 Salt bridges: A:R.252 Metal complexes: A:H.229 HEM.4: 22 residues within 4Å: Chain A: H.122, V.123, A.124, T.126, G.127, V.128, L.182, I.217, L.221, K.243, T.246, A.247, A.250, V.254, V.283, S.284, C.285, C.288, H.289, N.293, K.294, P.295 15 PLIP interactions: 15 interactions with chain A, Hydrophobic interactions: A:V.123, A:V.128, A:L.182, A:I.217, A:T.246, A:A.247, A:A.250, A:V.283 Hydrogen bonds: A:T.126, A:N.293 Salt bridges: A:K.243, A:K.294, A:K.294 Metal complexes: A:H.122, A:H.289

6 x BGL: 2-O-octyl-beta-D-glucopyranose(Non-covalent)

BGL.5: 5 residues within 4Å: Chain B: L.183, S.186 Chain C: F.90, I.178 Ligands: BCL.16 3 PLIP interactions: 1 interactions with chain B, 2 interactions with chain C Hydrogen bonds: B:S.186 Hydrophobic interactions: C:F.90, C:I.178 BGL.6: 5 residues within 4Å: Chain B: N.68, L.69, W.70 Ligands: BGL.7, PEF.21 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:W.70, B:W.70 Hydrogen bonds: B:L.69 BGL.7: 10 residues within 4Å: Chain B: W.70 Chain C: P.199, H.300, M.302 Chain D: Q.13, I.16, W.20 Ligands: BGL.6, BCL.9, PEF.21 3 PLIP interactions: 1 interactions with chain C, 1 interactions with chain D, 1 interactions with chain B Hydrogen bonds: C:H.300 Hydrophobic interactions: D:I.16, B:W.70 BGL.12: 6 residues within 4Å: Chain A: Y.152 Chain C: F.72, N.73, A.76, W.80, W.113 3 PLIP interactions: 3 interactions with chain C Hydrophobic interactions: C:F.72, C:W.113 Hydrogen bonds: C:A.76 BGL.13: 3 residues within 4Å: Chain C: L.126, W.129, A.150 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:L.126, C:A.150 BGL.14: 3 residues within 4Å: Chain C: W.270 Chain D: F.22, Y.29 6 PLIP interactions: 3 interactions with chain C, 3 interactions with chain D Hydrogen bonds: C:R.266, C:W.270, D:Y.29 Water bridges: C:H.144 Hydrophobic interactions: D:F.22, D:F.22

4 x BCL: BACTERIOCHLOROPHYLL A(Non-covalent)

BCL.8: 30 residues within 4Å: Chain B: F.105, A.132, A.135, Y.136, L.139, W.164, V.165, S.166, V.168, G.169, Y.170, F.175, H.176, H.181, A.184, I.185, F.188, S.252, A.253, C.255, I.256 Chain C: T.185, Y.196, Y.209 Ligands: BCL.9, BPH.10, BCL.16, BCL.17, MQ8.19, PEF.21 16 PLIP interactions: 15 interactions with chain B, 1 interactions with chain C, Hydrophobic interactions: B:F.105, B:F.105, B:F.105, B:Y.136, B:L.139, B:V.165, B:V.168, B:Y.170, B:F.175, B:A.184, B:I.185, B:I.185, B:F.188, C:Y.209 Hydrogen bonds: B:S.252 Metal complexes: B:H.181 BCL.9: 22 residues within 4Å: Chain B: V.46, I.49, Y.136, L.139, F.154, I.158, L.159, H.161, L.162, V.165 Chain C: Y.196, M.202, I.205, A.206, Y.209, G.210, L.213 Ligands: BGL.7, BCL.8, BPH.10, BCL.17, PEF.21 12 PLIP interactions: 8 interactions with chain B, 4 interactions with chain C, Hydrophobic interactions: B:V.46, B:I.49, B:Y.136, B:F.154, B:F.154, B:V.165, C:Y.196, C:I.205, C:I.205, C:L.213 pi-Stacking: B:F.154 Metal complexes: B:H.161 BCL.16: 23 residues within 4Å: Chain B: H.176, M.182, I.185, S.186, F.189, T.190, L.193, V.228 Chain C: W.128, F.155, Y.156, L.159, V.174, I.178, H.181, L.182, W.184, T.185 Ligands: BGL.5, BCL.8, BCL.17, BPH.18, CRT.20 13 PLIP interactions: 8 interactions with chain C, 5 interactions with chain B, Hydrophobic interactions: C:W.128, C:F.155, C:Y.156, C:L.159, C:V.174, C:L.182, C:W.184, B:I.185, B:I.185, B:L.193, B:V.228 Metal complexes: C:H.181 Hydrogen bonds: B:T.190 BCL.17: 30 residues within 4Å: Chain B: V.165, Y.170, F.189 Chain C: I.70, I.125, F.149, A.152, F.155, Y.156, L.159, T.185, A.186, F.188, S.189, L.195, Y.196, H.201, S.204, I.205, L.208, Y.209, V.276, A.279, G.282, I.283 Ligands: BCL.8, BCL.9, BCL.16, BPH.18, CRT.20 18 PLIP interactions: 17 interactions with chain C, 1 interactions with chain B, Hydrophobic interactions: C:I.70, C:F.149, C:F.155, C:F.155, C:F.155, C:Y.156, C:F.188, C:L.195, C:Y.196, C:Y.196, C:I.205, C:I.205, C:L.208, C:Y.209 Hydrogen bonds: C:S.204 Salt bridges: C:H.201 Metal complexes: C:H.201 pi-Cation interactions: B:H.176

2 x BPH: BACTERIOPHEOPHYTIN A(Non-covalent)

BPH.10: 30 residues within 4Å: Chain B: F.41, T.42, G.45, I.49, I.97, A.101, A.104, F.105, W.108, E.112, V.125, F.129, F.131, A.132, Y.136, F.154, Y.156, H.161, A.245, L.246, A.249 Chain C: Y.209, A.212, L.213, M.217, W.251, M.255 Ligands: BCL.8, BCL.9, MQ8.19 17 PLIP interactions: 15 interactions with chain B, 2 interactions with chain C Hydrophobic interactions: B:I.49, B:I.97, B:A.101, B:F.105, B:W.108, B:F.129, B:F.129, B:F.131, B:F.154, B:Y.156, B:Y.156, B:L.246, B:A.249, C:Y.209, C:A.212 Hydrogen bonds: B:E.112 pi-Stacking: B:F.129 BPH.18: 21 residues within 4Å: Chain B: F.189, C.192, L.193, S.196, M.197, I.227, V.228 Chain C: G.63, L.64, I.67, S.124, I.125, W.128, L.145, A.148, F.149, A.152, A.272, V.276 Ligands: BCL.16, BCL.17 8 PLIP interactions: 7 interactions with chain C, 1 interactions with chain B Hydrophobic interactions: C:I.67, C:A.148, C:F.149, C:A.152, C:V.276, C:V.276, B:L.193 pi-Stacking: C:F.149

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

LDA.11: 9 residues within 4Å: Chain B: L.83, R.84, M.85, W.94, Q.95, T.98, I.99, V.140, W.150 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:M.85, B:W.94, B:T.98, B:I.99, B:W.150 Hydrogen bonds: B:M.85, B:M.85

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

FE.15: 5 residues within 4Å: Chain B: H.198, H.238 Chain C: H.218, E.233, H.265 5 PLIP interactions: 2 interactions with chain B, 3 interactions with chain C Metal complexes: B:H.198, B:H.238, C:H.218, C:E.233, C:H.265

1 x MQ8: MENAQUINONE 8(Non-covalent)

MQ8.19: 23 residues within 4Å: Chain B: F.29, G.35, F.39, T.42, W.108 Chain C: L.213, M.217, H.218, T.221, A.247, A.248, W.251, M.255, F.257, N.258, A.259, T.260, M.261, I.264, W.267 Ligands: BCL.8, BPH.10, PEF.21 20 PLIP interactions: 12 interactions with chain C, 8 interactions with chain B Hydrophobic interactions: C:L.213, C:M.217, C:T.221, C:A.247, C:W.251, C:F.257, C:F.257, C:A.259, C:W.267, C:W.267, B:F.29, B:F.29, B:F.29, B:F.29, B:F.39, B:T.42, B:W.108, B:W.108 Hydrogen bonds: C:H.218, C:A.259

1 x CRT: SPIRILLOXANTHIN(Non-covalent)

CRT.20: 23 residues within 4Å: Chain C: I.67, I.70, G.71, F.72, F.89, I.105, W.114, L.115, G.118, L.119, T.122, Y.156, L.159, G.160, F.161, W.170, V.174, F.176, G.177, I.178, H.181 Ligands: BCL.16, BCL.17 20 PLIP interactions: 20 interactions with chain C Hydrophobic interactions: C:I.67, C:I.70, C:F.72, C:F.89, C:F.89, C:I.105, C:W.114, C:W.114, C:L.119, C:L.119, C:Y.156, C:Y.156, C:L.159, C:F.161, C:F.161, C:V.174, C:V.174, C:V.174, C:F.176, C:I.178

1 x PEF: DI-PALMITOYL-3-SN-PHOSPHATIDYLETHANOLAMINE(Non-covalent)

PEF.21: 16 residues within 4Å: Chain B: F.29 Chain C: F.207, R.252, M.255, G.256, F.257 Chain D: F.23, R.31, K.35, Y.39, L.41 Ligands: BGL.6, BGL.7, BCL.8, BCL.9, MQ8.19 10 PLIP interactions: 5 interactions with chain C, 5 interactions with chain D Hydrophobic interactions: C:F.207, C:F.257, C:F.257, C:F.257, D:F.23, D:F.23 Hydrogen bonds: C:G.256, D:R.31 Salt bridges: D:R.31, D:K.35

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Nogi, T. et al., Crystal structures of photosynthetic reaction center and high-potential iron-sulfur protein from Thermochromatium tepidum: thermostability and electron transfer. Proc.Natl.Acad.Sci.USA (2000)

Release Date

2000-12-13

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