SMTL ID : 2qjy.3 (2 other biounits)

Crystal structure of rhodobacter sphaeroides double mutant with stigmatellin and UQ2

Coordinates

PDB Format Compare

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 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:V.9, B:E.129 SR.17: 4 residues within 4Å: Chain E: D.8, V.9, E.14, E.129 3 PLIP interactions: 3 interactions with chain E Metal complexes: E:D.8, E:V.9, E:E.14

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

HEM.2: 23 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, G.220, N.221, N.222 Ligands: UQ2.6 21 PLIP interactions: 21 interactions with chain A, Hydrophobic interactions: A:L.51, A:L.51, A:F.104, A:F.104, A:I.112, A:W.129, A:I.135, A:Y.136, A:V.209, A:F.216, A:F.216 Hydrogen bonds: A:W.45, A:G.48, A:N.222 Water bridges: A:R.125, A:T.219 Salt bridges: A:H.111, A:R.114, A:R.125 Metal complexes: A:H.111, A:H.212 HEM.3: 22 residues within 4Å: Chain A: Q.58, I.59, G.62, I.63, L.65, A.66, Y.69, 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:Q.58, A:I.63, A:Y.69, A:A.98, A:A.101, A:T.142, A:L.149, A:L.149, A:F.195, A:Y.199, A:Y.199 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.9: 17 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 12 PLIP interactions: 12 interactions with chain B, Hydrophobic interactions: B:L.135, B:I.183, B:A.184, B:M.185 Hydrogen bonds: B:Y.130, B:Y.130, B:A.184 Salt bridges: B:R.107 pi-Stacking: B:H.40, B:H.40, B:H.40 Metal complexes: B:H.40 HEM.12: 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: UQ2.16 23 PLIP interactions: 23 interactions with chain D, Hydrophobic interactions: D:L.51, D:L.51, D:F.104, D:F.104, D:I.112, 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.47, D:N.221 Salt bridges: D:H.111, D:R.114, D:R.125 pi-Stacking: D:H.212 Metal complexes: D:H.111, D:H.212 HEM.13: 25 residues within 4Å: Chain D: Q.58, I.59, 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, F.195, H.198, Y.199, P.202, I.205, Y.297 26 PLIP interactions: 26 interactions with chain D, Hydrophobic interactions: D:Q.58, D:Q.58, D:I.59, D:L.65, D:A.66, D:Y.69, D:V.80, D:A.98, D:A.101, D:F.104, D:T.142, D:L.149, D:L.149, D:F.195, D:Y.199, D:I.205 Water bridges: D:R.94 Salt bridges: D:R.94, D:R.94 pi-Stacking: D:H.97, D:H.97, D:H.198, D:H.198, D:H.198 Metal complexes: D:H.97, D:H.198 HEM.18: 19 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, L.215 14 PLIP interactions: 14 interactions with chain E, Hydrophobic interactions: E:L.94, E:P.98, E:L.135, E:I.183, E:M.185, E:P.188, E:L.189, E:L.215 Hydrogen bonds: E:Y.130, E:A.184 Water bridges: E:N.162 Salt bridges: E:R.107 pi-Stacking: E:H.40 Metal complexes: E:H.40

2 x SMA: STIGMATELLIN A(Non-covalent)

SMA.4: 23 residues within 4Å: Chain A: L.137, M.140, A.141, F.144, M.145, M.154, G.158, V.161, I.162, L.180, F.194, L.197, I.292, V.293, P.294, E.295, F.298, Y.302, M.336, F.337, I.340 Chain F: C.151, H.152 14 PLIP interactions: 14 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:L.180, A:F.194, A:L.197, A:P.294, A:F.298, A:F.298, A:Y.302 Hydrogen bonds: A:E.295 SMA.14: 21 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.197, I.292, V.293, P.294, E.295, F.298, F.301, Y.302, M.336, F.337, I.340 11 PLIP interactions: 11 interactions with chain D Hydrophobic interactions: D:F.144, D:F.144, D:F.144, D:V.161, D:I.162, D:L.197, D:F.298, D:F.298, D:F.301, 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: 12 residues within 4Å: Chain A: M.44, L.103, I.106, F.113, R.114, Y.117, Y.118, F.263, R.358, F.367, W.368, F.374 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:L.103, A:I.106, A:F.113, A:F.113, A:F.113, A:F.367, A:F.374 Hydrogen bonds: A:Y.117, A:Y.118 Salt bridges: A:R.358 LOP.15: 14 residues within 4Å: Chain D: M.44, L.103, I.106, F.113, R.114, Y.117, Y.118, V.262, F.263, L.274, R.358, F.367, W.368, F.374 13 PLIP interactions: 13 interactions with chain D Hydrophobic interactions: 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:F.367, D:F.374 Hydrogen bonds: D:Y.118, D:Y.118 Salt bridges: D:R.358

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

UQ2.6: 11 residues within 4Å: Chain A: V.49, A.52, V.56, A.206, I.213, F.216, H.217, N.221, F.244, D.252 Ligands: HEM.2 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:A.52, A:V.56, A:A.206 Hydrogen bonds: A:N.221 pi-Stacking: A:F.244 UQ2.16: 10 residues within 4Å: Chain D: V.49, A.52, L.55, I.213, F.216, H.217, N.221, F.244, D.252 Ligands: HEM.12 3 PLIP interactions: 3 interactions with chain D Hydrophobic interactions: D:L.55, D:I.213 pi-Stacking: D:F.244

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

BGL.7: 8 residues within 4Å: Chain A: F.269 Chain B: E.14, G.15, P.16, L.121, N.123, G.124, K.227 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:G.15 Salt bridges: B:K.227 BGL.11: 9 residues within 4Å: Chain D: A.265, F.269 Chain E: F.13, E.14, G.15, P.16, N.123, G.124, K.227 5 PLIP interactions: 4 interactions with chain E, 1 interactions with chain D Hydrogen bonds: E:G.15, E:N.123, E:K.227 Salt bridges: E:K.227 Hydrophobic interactions: D:A.265

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.21: 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

1 x NA: SODIUM ION(Non-functional Binders)

NA.19: 3 residues within 4Å: Chain F: S.87, V.88, Q.92 2 PLIP interactions: 2 interactions with chain F Hydrogen bonds: F:S.87, F:Q.92

1 x CL: CHLORIDE ION(Non-functional Binders)

CL.20: 3 residues within 4Å: Chain F: V.88, Q.92, R.163 Ligand excluded by PLIP

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
M

D
P

B
N

E
Q

C
O

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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