SMTL ID : 2fyn.2 (2 other biounits)

Crystal Structure Analysis of the double mutant Rhodobacter Sphaeroides bc1 complex

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.20 Å

Oligo State

hetero-2-2-2-mer

Ligands

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

HEM.1: 25 residues within 4Å: Chain A: W.45, G.48, L.51, A.52, F.104, V.108, H.111, I.112, R.114, S.120, R.125, T.128, W.129, G.132, M.133, I.135, Y.136, I.205, V.209, H.212, 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:F.104, A:V.108, A:I.112, A:T.128, A:W.129, A:I.135, A:Y.136, A:I.205, A:V.209, A:V.209, A:F.216, A:F.216 Hydrogen bonds: A:G.48, A:N.221, A:N.222 Salt bridges: A:H.111, A:R.114, A:R.125 Metal complexes: A:H.111, A:H.212 HEM.2: 23 residues within 4Å: Chain A: Q.58, G.62, I.63, L.65, A.66, Y.69, V.80, R.94, H.97, A.98, A.101, F.104, T.142, A.143, G.146, Y.147, L.149, P.150, H.198, Y.199, P.202, I.205, Y.297 20 PLIP interactions: 20 interactions with chain A, Hydrophobic interactions: A:Q.58, A:Q.58, A:A.66, A:Y.69, A:A.98, A:A.101, A:F.104, A:F.104, A:T.142, A:L.149, A:L.149, A:Y.199, A:P.202, A:I.205 Salt bridges: A:R.94, A:R.94 pi-Stacking: A:H.97, A:H.198 Metal complexes: A:H.97, A:H.198 HEM.5: 19 residues within 4Å: Chain B: V.35, C.36, C.39, H.40, L.94, N.96, A.97, P.98, M.103, R.107, Y.130, L.135, F.160, I.183, A.184, M.185, P.188, V.211, L.215 13 PLIP interactions: 13 interactions with chain B, Hydrophobic interactions: B:L.135, B:I.183, B:M.185, B:P.188, B:V.211, B:L.215 Hydrogen bonds: B:Y.130, B:Y.130, B:A.184 Salt bridges: B:R.107 pi-Stacking: B:H.40 pi-Cation interactions: B:H.40 Metal complexes: B:H.40 HEM.7: 23 residues within 4Å: Chain D: W.45, G.48, L.51, A.52, F.104, V.108, H.111, I.112, R.114, S.120, R.125, T.128, W.129, G.132, M.133, I.135, Y.136, V.209, H.212, F.216, G.220, N.221, N.222 22 PLIP interactions: 22 interactions with chain D, Hydrophobic interactions: D:L.51, D:A.52, D:F.104, D:V.108, D:I.112, D:T.128, D:W.129, D:M.133, D:I.135, D:Y.136, D:V.209, D:V.209, D:F.216, D:F.216 Hydrogen bonds: D:G.48, D:N.221, D:N.222 Salt bridges: D:H.111, D:R.114, D:R.125 Metal complexes: D:H.111, D:H.212 HEM.8: 23 residues within 4Å: Chain D: Q.58, I.59, G.62, I.63, A.66, Y.69, V.80, R.94, H.97, A.101, F.104, T.142, A.143, G.146, Y.147, L.149, P.150, F.195, H.198, Y.199, P.202, I.205, Y.297 20 PLIP interactions: 20 interactions with chain D, Hydrophobic interactions: D:Q.58, D:I.59, D:Y.69, D:Y.69, D:A.101, D:F.104, D:T.142, D:L.149, D:L.149, D:F.195, D:Y.199, D:P.202, D:I.205 Salt bridges: D:R.94, D:R.94 pi-Stacking: D:H.97, D:H.198, D:H.198 Metal complexes: D:H.97, D:H.198 HEM.11: 20 residues within 4Å: Chain E: V.35, C.36, C.39, H.40, L.94, N.96, A.97, P.98, M.103, R.107, Y.130, I.131, L.135, F.160, I.183, A.184, M.185, P.188, V.211, L.215 11 PLIP interactions: 11 interactions with chain E, Hydrophobic interactions: E:I.131, E:L.135, E:I.183, E:M.185, E:P.188, E:V.211, E:L.215 Hydrogen bonds: E:Y.130, E:A.184 Salt bridges: E:R.107 Metal complexes: E:H.40

2 x SMA: STIGMATELLIN A(Non-covalent)

SMA.3: 18 residues within 4Å: Chain A: M.140, F.144, M.145, G.158, V.161, I.162, F.194, I.292, V.293, P.294, E.295, F.298, Y.302, M.336, F.337, I.340 Chain F: C.151, H.152 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:F.144, A:F.144, A:F.144, A:V.161, A:I.162, A:I.162, A:F.194, A:F.298, A:F.298, A:Y.302 Hydrogen bonds: A:E.295 SMA.9: 20 residues within 4Å: Chain C: C.151, H.152 Chain D: L.137, M.140, A.141, F.144, M.145, G.158, V.161, I.162, L.180, I.292, V.293, P.294, E.295, F.298, Y.302, M.336, F.337, I.340 10 PLIP interactions: 10 interactions with chain D Hydrophobic interactions: D:F.144, D:F.144, D:F.144, D:V.161, D:I.162, D:I.162, D:L.180, D:F.298, D:F.298 Hydrogen bonds: D:E.295

2 x LOP: (1R)-2-{[(R)-(2-AMINOETHOXY)(HYDROXY)PHOSPHORYL]OXY}-1-[(DODECANOYLOXY)METHYL]ETHYL (9Z)-OCTADEC-9-ENOATE(Non-covalent)

LOP.4: 13 residues within 4Å: Chain A: M.44, W.47, N.99, L.103, I.106, F.113, R.114, Y.117, Y.118, F.263, R.358, F.367, W.368 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:W.47, A:W.47, A:L.103, A:L.103, A:F.113, A:F.113, A:F.263, A:F.367 Hydrogen bonds: A:Y.117, A:Y.118 Salt bridges: A:R.358 LOP.10: 14 residues within 4Å: Chain D: N.42, M.44, L.110, F.113, R.114, Y.117, Y.118, V.262, F.263, I.266, R.358, W.368, F.374, V.375 10 PLIP interactions: 10 interactions with chain D Hydrophobic interactions: D:F.113, D:F.113, D:V.262, D:F.263, D:I.266, D:F.374 Hydrogen bonds: D:N.42, D:Y.118 Salt bridges: D:R.358, D:K.364

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

FES.6: 10 residues within 4Å: Chain C: C.129, H.131, L.132, G.133, C.134, C.149, C.151, H.152, G.153, S.154 4 PLIP interactions: 4 interactions with chain C, Metal complexes: C:C.129, C:H.131, C:C.149, C:H.152 FES.12: 9 residues within 4Å: Chain F: C.129, H.131, L.132, G.133, C.134, C.149, H.152, G.153, S.154 4 PLIP interactions: 4 interactions with chain F, Metal complexes: F:C.129, F:H.131, F:C.149, F:H.152

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Esser, L. et al., Surface-modulated motion switch: Capture and release of iron-sulfur protein in the cytochrome bc1 complex. Proc.Natl.Acad.Sci.Usa (2006)

Release Date

2006-08-29

Peptides

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

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
G

D
J

B
H

E
K

C
I

F
L

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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