SMTL ID : 2qjy.1 (2 other biounits)

Crystal structure of rhodobacter sphaeroides double mutant with stigmatellin and UQ2

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.40 Å

Oligo State

hetero-2-2-2-mer

Ligands

3 x SR: STRONTIUM ION(Non-functional Binders)

SR.1: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) SR.8: 4 residues within 4Å: Chain B: D.8, V.9, E.14, E.129 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:D.8, B:V.9, B:E.14 SR.17: 4 residues within 4Å: Chain E: D.8, V.9, E.14, E.129 4 PLIP interactions: 4 interactions with chain E Metal complexes: E:D.8, E:V.9, E:E.14, E:E.129

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

HEM.2: 24 residues within 4Å: Chain A: W.45, G.48, L.51, A.52, F.104, 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, T.219, G.220, N.221, N.222 Ligands: UQ2.6 23 PLIP interactions: 23 interactions with chain A, Hydrophobic interactions: A:L.51, A:L.51, A:F.104, A:I.112, A:W.129, A:W.129, A:I.135, A:Y.136, A:V.209, A:F.216, A:F.216, A:F.216 Hydrogen bonds: A:W.45, A:G.48, A:T.219, A:T.219, A:N.222 Water bridges: A:N.222 Salt bridges: A:H.111, A:R.114, A:R.125 Metal complexes: A:H.111, A:H.212 HEM.3: 23 residues within 4Å: Chain A: Q.58, I.59, G.62, I.63, L.65, A.66, Y.69, V.80, R.94, H.97, A.98, A.101, T.142, A.143, G.146, Y.147, L.149, P.150, F.195, H.198, Y.199, P.202, Y.297 18 PLIP interactions: 18 interactions with chain A, Hydrophobic interactions: A:Q.58, A:I.59, A:L.65, A:A.66, A:Y.69, A:V.80, A:A.98, A:A.101, A:T.142, A:L.149, A:L.149, A:F.195, A:Y.199 Water bridges: A:R.94 Salt bridges: A:R.94, A:R.94 Metal complexes: A:H.97, A:H.198 HEM.9: 18 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, L.189 13 PLIP interactions: 13 interactions with chain B, Hydrophobic interactions: B:P.98, B:L.135, B:I.183, B:A.184, B:M.185, B:P.188, B:L.189 Hydrogen bonds: B:Y.130, B:Y.130, B:A.184 Salt bridges: B:R.107 pi-Cation interactions: B:H.40 Metal complexes: B:H.40 HEM.11: 24 residues within 4Å: Chain D: W.45, G.48, L.51, A.52, F.104, 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, T.219, G.220, N.221, N.222 Ligands: UQ2.15 23 PLIP interactions: 23 interactions with chain D, Hydrophobic interactions: D:L.51, D:L.51, D:F.104, D:I.112, D:T.128, D:W.129, D:W.129, D:I.135, D:Y.136, D:V.209, D:F.216, D:F.216 Hydrogen bonds: D:G.48, D:T.219, D:T.219, D:N.222 Water bridges: D:W.45, D:W.47 Salt bridges: D:H.111, D:R.114, D:R.125 Metal complexes: D:H.111, D:H.212 HEM.12: 22 residues within 4Å: Chain D: Q.58, I.59, G.62, I.63, L.65, A.66, Y.69, R.94, H.97, A.101, T.142, A.143, G.146, Y.147, L.149, P.150, F.195, H.198, Y.199, P.202, I.205, Y.297 18 PLIP interactions: 18 interactions with chain D, Hydrophobic interactions: D:Q.58, D:Q.58, D:I.63, D:Y.69, D:A.101, D:T.142, D:L.149, D:L.149, D:F.195, D:Y.199, D:Y.199, D:I.205 Water bridges: D:R.94 Salt bridges: D:R.94, D:R.94 pi-Stacking: D:H.97 Metal complexes: D:H.97, D:H.198 HEM.18: 18 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, L.135, F.160, I.183, A.184, M.185, P.188, L.189 11 PLIP interactions: 11 interactions with chain E, Hydrophobic interactions: E:P.98, E:L.135, E:I.183, E:M.185, E:P.188, E:L.189 Hydrogen bonds: E:Y.130, E:A.184 Salt bridges: E:R.107 pi-Stacking: E:H.40 Metal complexes: E:H.40

2 x SMA: STIGMATELLIN A(Non-covalent)

SMA.4: 22 residues within 4Å: Chain A: L.137, M.140, A.141, F.144, M.145, M.154, G.158, V.161, I.162, F.194, L.197, I.292, P.294, E.295, F.298, F.301, Y.302, M.336, F.337, I.340 Chain F: C.151, H.152 15 PLIP interactions: 15 interactions with chain A Hydrophobic interactions: A:A.141, A:F.144, A:F.144, A:F.144, A:V.161, A:I.162, A:I.162, A:F.194, A:L.197, A:P.294, A:F.298, A:F.298, A:F.301, A:Y.302 Hydrogen bonds: A:E.295 SMA.13: 20 residues within 4Å: Chain C: C.151, H.152 Chain D: L.137, M.140, A.141, F.144, M.154, G.158, V.161, I.162, L.180, F.194, I.292, P.294, E.295, F.298, Y.302, M.336, F.337, I.340 12 PLIP interactions: 12 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.194, D:F.298, D:F.298, D:Y.302 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.5: 15 residues within 4Å: Chain A: M.44, L.103, I.106, F.113, R.114, Y.117, Y.118, V.262, I.266, L.274, W.296, R.358, W.368, F.374, V.375 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:L.103, A:F.113, A:V.262, A:I.266, A:L.274, A:W.296, A:W.368, A:F.374, A:F.374, A:V.375 Hydrogen bonds: A:Y.117, A:Y.118, A:Y.118 Salt bridges: A:R.358 LOP.14: 16 residues within 4Å: Chain D: M.44, W.47, L.103, I.106, F.113, R.114, Y.117, Y.118, V.262, F.263, L.274, W.296, R.358, F.367, W.368, F.374 13 PLIP interactions: 13 interactions with chain D Hydrophobic interactions: D:W.47, D:L.103, D:L.103, D:I.106, D:F.113, D:F.113, D:V.262, D:F.263, D:L.274, D:W.296, D:F.367 Hydrogen bonds: D:Y.118 Salt bridges: D:R.358

2 x UQ2: UBIQUINONE-2(Non-covalent)

UQ2.6: 9 residues within 4Å: Chain A: T.32, I.35, V.49, A.52, I.213, F.216, H.217, F.244 Ligands: HEM.2 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:A.52, A:I.213 pi-Stacking: A:F.244 UQ2.15: 11 residues within 4Å: Chain D: T.32, V.49, A.52, A.206, I.213, F.216, H.217, N.221, F.244, D.252 Ligands: HEM.11 3 PLIP interactions: 3 interactions with chain D Hydrophobic interactions: D:T.32, D:A.52 pi-Stacking: D:F.244

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

BGL.7: 11 residues within 4Å: Chain A: A.265, F.269, M.270 Chain B: F.13, E.14, G.15, P.16, N.123, G.124, M.216, K.227 6 PLIP interactions: 4 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:G.15, B:G.15, B:N.123 Salt bridges: B:K.227 Hydrophobic interactions: A:A.265, A:F.269 BGL.16: 8 residues within 4Å: Chain D: I.266, F.269 Chain E: F.13, E.14, G.15, P.16, G.124, K.227 6 PLIP interactions: 4 interactions with chain E, 2 interactions with chain D Hydrogen bonds: E:G.15, E:N.123, E:K.227 Salt bridges: E:K.227 Hydrophobic interactions: D:I.266, D:F.269

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

FES.10: 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.19: 10 residues within 4Å: Chain F: 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 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., Inhibitor-complexed Structures of the Cytochrome bc1 from the Photosynthetic Bacterium Rhodobacter sphaeroides. J.Biol.Chem. (2008)

Release Date

2007-12-25

Peptides

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

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

D
D

B
B

E
E

C
C

F
F

Membrane

We predict this structure to be a membrane protein.
Show / Hide

Cytochrome b

Cytochrome c1

Ubiquinol-cytochrome c reductase iron-sulfur subunit

Related Entries With Identical Sequence