SMTL ID : 1zrt.1

Rhodobacter capsulatus cytochrome bc1 complex with stigmatellin bound

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 3.51 Å

Oligo State

hetero-2-2-2-mer

Ligands

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

HEM.1: 22 residues within 4Å: Chain A: L.55, Q.58, G.62, I.63, L.65, A.66, R.94, H.97, A.98, A.101, F.104, T.142, A.143, G.146, Y.147, L.149, P.150, F.195, H.198, Y.199, P.202, Y.297 19 PLIP interactions: 19 interactions with chain A, Hydrophobic interactions: A:L.55, A:Q.58, A:L.65, A:L.65, A:A.66, A:A.98, A:F.104, A:F.104, A:T.142, A:A.143, A:L.149, A:F.195, A:Y.199, A:Y.199 Hydrogen bonds: A:N.279 Salt bridges: A:R.94, A:R.94 Metal complexes: A:H.97, A:H.198 HEM.2: 24 residues within 4Å: Chain A: W.45, G.48, L.51, A.52, V.108, H.111, I.112, R.114, S.120, R.125, T.128, W.129, G.132, M.133, I.135, M.139, V.209, H.212, I.213, F.216, T.219, G.220, N.221, N.222 22 PLIP interactions: 22 interactions with chain A, Hydrophobic interactions: A:L.51, A:L.51, A:A.52, A:I.112, A:T.128, A:W.129, A:I.135, A:V.209, A:I.213, A:F.216, A:F.216, A:F.216 Hydrogen bonds: A:W.45, A:I.49, A:R.114, A:T.219, A:N.222 Salt bridges: A:H.111, A:R.114, A:R.125 Metal complexes: A:H.111, A:H.212 HEM.8: 23 residues within 4Å: Chain D: L.55, Q.58, G.62, I.63, L.65, A.66, Y.69, R.94, H.97, A.98, A.101, F.104, T.142, A.143, G.146, Y.147, L.149, P.150, F.195, H.198, Y.199, P.202, Y.297 21 PLIP interactions: 21 interactions with chain D, Hydrophobic interactions: D:L.55, D:Q.58, D:L.65, D:L.65, D:A.66, D:Y.69, D:A.98, D:F.104, D:F.104, D:T.142, D:A.143, D:L.149, D:F.195, D:Y.199, D:Y.199, D:P.202, D:P.202 Salt bridges: D:R.94, D:R.94 Metal complexes: D:H.97, D:H.198 HEM.9: 23 residues within 4Å: Chain D: W.45, G.48, L.51, A.52, V.108, H.111, I.112, R.114, S.120, R.125, T.128, W.129, G.132, M.133, I.135, M.139, V.209, H.212, F.216, T.219, G.220, N.221, N.222 19 PLIP interactions: 19 interactions with chain D, Hydrophobic interactions: D:L.51, D:L.51, D:A.52, D:I.112, D:T.128, D:W.129, D:I.135, D:V.209, D:F.216, D:F.216 Hydrogen bonds: D:W.45, D:I.49, D:R.114, D:N.222 Salt bridges: D:H.111, D:R.114, D:R.125 Metal complexes: D:H.111, D:H.212

2 x SMA: STIGMATELLIN A(Non-covalent)

SMA.3: 21 residues within 4Å: Chain A: L.137, M.140, G.141, F.144, M.154, G.158, V.161, I.162, L.165, F.166, L.180, F.194, I.292, V.293, P.294, E.295, F.298, Y.302, M.336, F.337 Chain F: H.156 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:F.144, A:F.144, A:F.144, A:L.165, A:F.166, A:L.180, A:F.194, A:F.298, A:F.298, A:F.298 Hydrogen bonds: A:E.295, A:E.295 SMA.10: 23 residues within 4Å: Chain C: C.155, H.156 Chain D: L.137, M.140, G.141, F.144, M.154, G.158, V.161, I.162, L.165, F.166, L.180, F.194, I.292, P.294, E.295, F.298, F.301, Y.302, M.336, F.337, I.340 17 PLIP interactions: 17 interactions with chain D Hydrophobic interactions: D:M.140, D:F.144, D:F.144, D:V.161, D:I.162, D:L.165, D:F.166, D:L.180, D:L.180, D:F.194, D:F.298, D:F.298, D:F.298, D:F.301 Hydrogen bonds: D:E.295, D:E.295, D:E.295

4 x UNL: UNKNOWN LIGAND(Covalent)(Non-covalent)

UNL.4: 6 residues within 4Å: Chain A: N.88, W.91, A.92 Chain B: K.220 Chain C: W.32, N.36 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain C Hydrophobic interactions: A:W.91, A:A.92 Hydrogen bonds: C:W.32 UNL.5: 4 residues within 4Å: Chain A: D.311, V.312, W.313, W.391 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:W.313, A:W.313, A:W.391 Hydrogen bonds: A:W.313 UNL.11: 10 residues within 4Å: Chain D: W.91, A.92, M.93, I.96 Chain E: K.220, A.223 Chain F: W.32, P.33, N.36 Ligands: PG6.14 9 PLIP interactions: 2 interactions with chain E, 3 interactions with chain D, 4 interactions with chain F Hydrophobic interactions: E:A.223, D:W.91, D:A.92, D:I.96, F:P.33, F:P.33 Hydrogen bonds: E:K.220, F:W.32, F:N.36 UNL.12: 5 residues within 4Å: Chain D: D.311, V.312, W.313, W.391, L.394 4 PLIP interactions: 4 interactions with chain D Hydrophobic interactions: D:W.313, D:W.391, D:L.394 Hydrogen bonds: D:W.313

2 x HEC: HEME C(Covalent)

HEC.6: 19 residues within 4Å: Chain B: V.33, C.34, C.37, H.38, G.95, M.96, G.97, P.98, R.107, Y.130, I.131, Y.134, F.158, I.160, A.181, R.182, M.183, P.184, P.186 13 PLIP interactions: 13 interactions with chain B, Hydrophobic interactions: B:P.98, B:I.131, B:M.183, B:P.184, B:P.186 Hydrogen bonds: B:Y.134, B:Y.134, B:R.182 Salt bridges: B:R.107, B:R.182 pi-Stacking: B:H.38, B:Y.134 Metal complexes: B:H.38 HEC.13: 19 residues within 4Å: Chain E: V.33, C.34, C.37, H.38, G.95, M.96, G.97, P.98, R.107, Y.130, I.131, Y.134, V.135, F.158, A.181, R.182, M.183, P.184, P.186 13 PLIP interactions: 13 interactions with chain E, Hydrophobic interactions: E:P.98, E:I.131, E:V.135, E:P.184, E:P.186 Hydrogen bonds: E:Y.130, E:Y.134, E:R.182 Salt bridges: E:R.107, E:R.182 pi-Stacking: E:H.38, E:Y.134 Metal complexes: E:H.38

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

FES.7: 10 residues within 4Å: Chain C: C.133, H.135, L.136, G.137, C.138, C.153, C.155, H.156, G.157, S.158 4 PLIP interactions: 4 interactions with chain C, Metal complexes: C:C.133, C:H.135, C:C.153, C:H.156 FES.15: 8 residues within 4Å: Chain F: C.133, H.135, L.136, C.153, C.155, H.156, G.157, S.158 4 PLIP interactions: 4 interactions with chain F, Metal complexes: F:C.133, F:H.135, F:C.153, F:H.156

1 x PG6: 1-(2-METHOXY-ETHOXY)-2-{2-[2-(2-METHOXY-ETHOXY]-ETHOXY}-ETHANE(Non-covalent)

PG6.14: 8 residues within 4Å: Chain D: F.53, L.260, F.264 Chain E: V.230 Chain F: V.26, A.30, W.32 Ligands: UNL.11 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Berry, E.A. et al., X-Ray Structure of Rhodobacter Capsulatus Cytochrome bc (1): Comparison with its Mitochondrial and Chloroplast Counterparts. Photosynth.Res. (2004)

Release Date

2005-06-07

Peptides

Cytochrome b: AD
Cytochrome c1: BE
Ubiquinol-cytochrome c reductase iron-sulfur subunit: CF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

D
P

B
D

E
Q

C
E

F
R

Membrane

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

Cytochrome c1

Ubiquinol-cytochrome c reductase iron-sulfur subunit

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