SMTL ID : 1p84.1 (1 other biounit)

HDBT inhibited Yeast Cytochrome bc1 Complex

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

hetero-2-2-2-2-2-2-2-2-2-mer

Ligands

4 x 3PH: 1,2-DIACYL-GLYCEROL-3-SN-PHOSPHATE(Non-covalent)

3PH.1: 10 residues within 4Å: Chain A: S.424, M.429 Chain C: I.226, F.227, L.230 Chain E: V.30, M.33, S.37 Ligands: UMQ.2, 3PH.10 6 PLIP interactions: 4 interactions with chain C, 2 interactions with chain A Hydrophobic interactions: C:I.226, C:F.227, C:L.230 Salt bridges: C:H.222 Hydrogen bonds: A:S.424, A:S.424 3PH.10: 14 residues within 4Å: Chain C: I.77, M.237, F.245 Chain D: L.208, K.211, T.212, I.215, L.216 Chain E: S.37, G.40, A.41, S.43, T.44 Ligands: 3PH.1 3 PLIP interactions: 2 interactions with chain D, 1 interactions with chain E Hydrophobic interactions: D:L.216 Salt bridges: D:K.211 Hydrogen bonds: E:S.43 3PH.14: 10 residues within 4Å: Chain J: S.424, M.429 Chain L: I.226, F.227, L.230 Chain N: V.30, M.33, S.37 Ligands: UMQ.15, 3PH.23 6 PLIP interactions: 4 interactions with chain L, 2 interactions with chain J Hydrophobic interactions: L:I.226, L:F.227, L:L.230 Salt bridges: L:H.222 Hydrogen bonds: J:S.424, J:S.424 3PH.23: 14 residues within 4Å: Chain L: I.77, M.237, F.245 Chain M: L.208, K.211, T.212, I.215, L.216 Chain N: S.37, G.40, A.41, S.43, T.44 Ligands: 3PH.14 3 PLIP interactions: 2 interactions with chain M, 1 interactions with chain N Hydrophobic interactions: M:L.216 Salt bridges: M:K.211 Hydrogen bonds: N:S.43

2 x UMQ: UNDECYL-MALTOSIDE(Non-covalent)

UMQ.2: 15 residues within 4Å: Chain A: W.401, D.402, S.427, M.428, M.429, R.430 Chain E: Y.27, V.30, S.38 Chain I: N.11, A.12, V.13, F.14, V.15 Ligands: 3PH.1 10 PLIP interactions: 4 interactions with chain I, 4 interactions with chain A, 2 interactions with chain E Hydrophobic interactions: I:V.15 Hydrogen bonds: I:N.11, I:A.12, I:V.15, A:S.427, A:M.428, A:R.430, A:R.430, E:Y.27, E:Y.27 UMQ.15: 15 residues within 4Å: Chain J: W.401, D.402, S.427, M.428, M.429, R.430 Chain N: Y.27, V.30, S.38 Chain R: N.11, A.12, V.13, F.14, V.15 Ligands: 3PH.14 11 PLIP interactions: 4 interactions with chain R, 4 interactions with chain J, 3 interactions with chain N Hydrophobic interactions: R:V.15 Hydrogen bonds: R:N.11, R:A.12, R:V.15, J:S.427, J:M.428, J:R.430, J:R.430, N:Y.27, N:Y.27, N:Y.27

6 x HEC: HEME C(Non-covalent)(Covalent)

HEC.3: 19 residues within 4Å: Chain C: L.40, Q.43, G.47, I.48, M.50, A.51, R.79, H.82, A.83, A.86, F.89, T.127, A.128, G.131, Y.132, V.135, H.183, Y.184, P.187 15 PLIP interactions: 15 interactions with chain C, Hydrophobic interactions: C:L.40, C:Q.43, C:A.51, C:A.83, C:A.86, C:F.89, C:T.127, C:Y.184 Salt bridges: C:R.79, C:R.79 pi-Stacking: C:H.82, C:H.183 pi-Cation interactions: C:H.183 Metal complexes: C:H.82, C:H.183 HEC.4: 21 residues within 4Å: Chain C: W.30, G.33, L.36, G.37, M.93, H.96, M.97, K.99, S.105, L.113, W.114, G.117, V.118, I.120, V.194, H.197, L.198, L.201, S.206, S.207 Ligands: UQ6.6 25 PLIP interactions: 25 interactions with chain C, Hydrophobic interactions: C:L.36, C:L.36, C:L.113, C:W.114, C:W.114, C:I.120, C:V.194, C:V.194, C:L.198, C:L.201 Hydrogen bonds: C:W.30, C:G.33, C:S.105, C:S.207 Water bridges: C:M.32, C:S.34 Salt bridges: C:H.96, C:K.99, C:K.99 pi-Stacking: C:H.96, C:H.96, C:H.197, C:H.197 Metal complexes: C:H.96, C:H.197 HEC.9: 20 residues within 4Å: Chain D: V.39, C.40, C.43, H.44, N.108, P.113, P.114, L.116, I.119, R.123, Y.129, I.130, L.134, F.157, I.162, A.163, M.164, V.167, L.168, L.194 17 PLIP interactions: 17 interactions with chain D, Hydrophobic interactions: D:P.113, D:P.114, D:L.116, D:I.119, D:I.130, D:L.134, D:I.162, D:M.164, D:V.167, D:V.167, D:L.168, D:L.194 Hydrogen bonds: D:Y.129, D:A.163 Salt bridges: D:R.123 pi-Stacking: D:H.44 Metal complexes: D:H.44 HEC.16: 19 residues within 4Å: Chain L: L.40, Q.43, G.47, I.48, M.50, A.51, R.79, H.82, A.83, A.86, F.89, T.127, A.128, G.131, Y.132, V.135, H.183, Y.184, P.187 15 PLIP interactions: 15 interactions with chain L, Hydrophobic interactions: L:L.40, L:Q.43, L:A.51, L:A.83, L:A.86, L:F.89, L:T.127, L:Y.184 Salt bridges: L:R.79, L:R.79 pi-Stacking: L:H.82, L:H.183 pi-Cation interactions: L:H.183 Metal complexes: L:H.82, L:H.183 HEC.17: 21 residues within 4Å: Chain L: W.30, G.33, L.36, G.37, M.93, H.96, M.97, K.99, S.105, L.113, W.114, G.117, V.118, I.120, V.194, H.197, L.198, L.201, S.206, S.207 Ligands: UQ6.19 25 PLIP interactions: 25 interactions with chain L, Hydrophobic interactions: L:L.36, L:L.36, L:L.113, L:W.114, L:W.114, L:I.120, L:V.194, L:V.194, L:L.198, L:L.201 Hydrogen bonds: L:W.30, L:G.33, L:S.105, L:S.207 Water bridges: L:M.32, L:S.34 Salt bridges: L:H.96, L:K.99, L:K.99 pi-Stacking: L:H.96, L:H.96, L:H.197, L:H.197 Metal complexes: L:H.96, L:H.197 HEC.22: 20 residues within 4Å: Chain M: V.39, C.40, C.43, H.44, N.108, P.113, P.114, L.116, I.119, R.123, Y.129, I.130, L.134, F.157, I.162, A.163, M.164, V.167, L.168, L.194 18 PLIP interactions: 18 interactions with chain M, Hydrophobic interactions: M:P.113, M:P.114, M:L.116, M:I.119, M:I.130, M:L.134, M:I.162, M:M.164, M:V.167, M:V.167, M:L.168, M:L.194 Hydrogen bonds: M:Y.129, M:Y.129, M:A.163 Salt bridges: M:R.123 pi-Stacking: M:H.44 Metal complexes: M:H.44

2 x DBT: 5-HEPTYL-6-HYDROXY-1,3-BENZOTHIAZOLE-4,7-DIONE(Non-covalent)

DBT.5: 15 residues within 4Å: Chain C: M.139, W.142, G.143, V.146, I.147, I.269, P.271, L.275, F.278, Y.279, L.282, M.295, I.299 Chain N: C.150, H.151 6 PLIP interactions: 6 interactions with chain C Hydrophobic interactions: C:I.147, C:P.271, C:L.275, C:F.278, C:Y.279, C:I.299 DBT.18: 15 residues within 4Å: Chain E: C.150, H.151 Chain L: M.139, W.142, G.143, V.146, I.147, I.269, P.271, L.275, F.278, Y.279, L.282, M.295, I.299 6 PLIP interactions: 6 interactions with chain L Hydrophobic interactions: L:I.147, L:P.271, L:L.275, L:F.278, L:Y.279, L:I.299

2 x UQ6: 5-(3,7,11,15,19,23-HEXAMETHYL-TETRACOSA-2,6,10,14,18,22-HEXAENYL)-2,3-DIMETHOXY-6-METHYL-BENZENE-1,4-DIOL(Non-covalent)

UQ6.6: 13 residues within 4Å: Chain C: Y.16, Q.22, I.26, S.34, G.37, L.40, I.44, L.201, S.206, M.221, D.229 Chain L: L.185 Ligands: HEC.4 4 PLIP interactions: 3 interactions with chain C, 1 interactions with chain L Hydrophobic interactions: C:L.40, C:I.44, L:L.185 Hydrogen bonds: C:Q.22 UQ6.19: 13 residues within 4Å: Chain C: L.185 Chain L: Y.16, Q.22, I.26, S.34, G.37, L.40, I.44, L.201, S.206, M.221, D.229 Ligands: HEC.17 4 PLIP interactions: 3 interactions with chain L, 1 interactions with chain C Hydrophobic interactions: L:L.40, L:I.44, C:L.185 Hydrogen bonds: L:Q.22

4 x 3PE: 1,2-Distearoyl-sn-glycerophosphoethanolamine(Non-covalent)

3PE.7: 14 residues within 4Å: Chain C: W.29, F.94, M.97, A.98, Y.102, Y.103, F.326, F.327, F.329, F.333, Y.359 Chain G: E.80 Chain H: R.50, F.51 8 PLIP interactions: 6 interactions with chain C, 1 interactions with chain H, 1 interactions with chain G Hydrophobic interactions: C:W.29, C:F.94, C:F.326, C:F.329, C:F.333, H:F.51 Hydrogen bonds: C:Y.103, G:E.80 3PE.8: 9 residues within 4Å: Chain C: F.3, N.7, Y.9, V.13, I.195 Chain L: T.112, N.115, I.119, M.196 8 PLIP interactions: 3 interactions with chain L, 5 interactions with chain C Hydrophobic interactions: L:I.119, C:V.13, C:I.195 Hydrogen bonds: L:T.112, L:N.115, C:N.7 Water bridges: C:S.6, C:V.8 3PE.20: 14 residues within 4Å: Chain L: W.29, F.94, M.97, A.98, Y.102, Y.103, F.326, F.327, F.329, F.333, Y.359 Chain P: E.80 Chain Q: R.50, F.51 9 PLIP interactions: 7 interactions with chain L, 1 interactions with chain Q, 1 interactions with chain P Hydrophobic interactions: L:W.29, L:F.94, L:F.326, L:F.329, L:F.333, Q:F.51 Hydrogen bonds: L:Y.102, L:Y.103, P:E.80 3PE.21: 9 residues within 4Å: Chain C: T.112, N.115, I.119, M.196 Chain L: F.3, N.7, Y.9, V.13, I.195 7 PLIP interactions: 5 interactions with chain L, 2 interactions with chain C Hydrophobic interactions: L:V.13, L:I.195, C:I.119 Hydrogen bonds: L:N.7, C:N.115 Water bridges: L:S.6, L:V.8

2 x PC1: 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE(Non-covalent)

PC1.11: 12 residues within 4Å: Chain C: L.251, G.252, H.253, S.268, V.270, W.273, L.276, G.337, Q.338, A.341 Chain D: H.124 Ligands: CDL.12 8 PLIP interactions: 7 interactions with chain C, 1 interactions with chain D Hydrophobic interactions: C:L.251, C:W.273, C:W.273, C:L.276, C:A.341 Hydrogen bonds: C:S.268 Salt bridges: C:H.253, D:H.124 PC1.24: 12 residues within 4Å: Chain L: L.251, G.252, H.253, S.268, V.270, W.273, L.276, G.337, Q.338, A.341 Chain M: H.124 Ligands: CDL.25 8 PLIP interactions: 7 interactions with chain L, 1 interactions with chain M Hydrophobic interactions: L:L.251, L:W.273, L:W.273, L:L.276, L:A.341 Hydrogen bonds: L:S.268 Salt bridges: L:H.253, M:H.124

2 x CDL: CARDIOLIPIN(Non-covalent)

CDL.12: 17 residues within 4Å: Chain C: N.27, Y.28, W.29, M.32, M.91, M.95, V.231, T.232, L.235, F.236, I.239 Chain D: Y.220, I.224, K.227, K.228 Chain G: H.83 Ligands: PC1.11 13 PLIP interactions: 6 interactions with chain C, 1 interactions with chain G, 6 interactions with chain D Hydrophobic interactions: C:Y.28, C:T.232, C:L.235, C:I.239 Hydrogen bonds: C:Y.28, C:Y.28, D:Y.220 Salt bridges: G:H.83, D:K.227, D:K.228 Water bridges: D:K.227, D:K.227, D:K.227 CDL.25: 17 residues within 4Å: Chain L: N.27, Y.28, W.29, M.32, M.91, M.95, V.231, T.232, L.235, F.236, I.239 Chain M: Y.220, I.224, K.227, K.228 Chain P: H.83 Ligands: PC1.24 11 PLIP interactions: 5 interactions with chain L, 1 interactions with chain P, 5 interactions with chain M Hydrophobic interactions: L:Y.28, L:T.232, L:L.235, L:I.239 Hydrogen bonds: L:Y.28 Salt bridges: P:H.83, M:K.227, M:K.228 Water bridges: M:K.227, M:K.227, M:K.227

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

FES.13: 10 residues within 4Å: Chain E: C.129, H.131, L.132, G.133, C.134, C.148, C.150, H.151, G.152, S.153 4 PLIP interactions: 4 interactions with chain E, Metal complexes: E:C.129, E:H.131, E:C.148, E:H.151 FES.26: 10 residues within 4Å: Chain N: C.129, H.131, L.132, G.133, C.134, C.148, C.150, H.151, G.152, S.153 4 PLIP interactions: 4 interactions with chain N, Metal complexes: N:C.129, N:H.131, N:C.148, N:H.151

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Palsdottir, H. et al., Structure of the yeast cytochrome bc1 complex with a hydroxyquinone anion Qo site inhibitor bound. J.Biol.Chem. (2003)

Release Date

2003-07-29

Peptides

Ubiquinol-cytochrome C reductase complex core protein I: AJ
Ubiquinol-cytochrome C reductase complex core protein 2: BK
cytochrome b: CL
Cytochrome c1, heme protein: DM
Ubiquinol-cytochrome C reductase iron-sulfur subunit: EN
Ubiquinol-cytochrome C reductase complex 17 kDa protein: FO
Ubiquinol-cytochrome C reductase complex 14 kDa protein: GP
Ubiquinol-cytochrome C reductase complex ubiquinone-binding protein QP-C: HQ
Ubiquinol-cytochrome C reductase complex 7.3 kDa protein: IR

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

J
A

B
B

K
B

C
C

L
C

D
D

M
D

E
E

N
E

F
F

O
F

G
G

P
G

H
H

Q
H

I
I

R
I

Membrane

We predict this structure to be a membrane protein.
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Ubiquinol-cytochrome C reductase complex core protein I

Ubiquinol-cytochrome C reductase complex core protein 2

cytochrome b

Cytochrome c1, heme protein

Ubiquinol-cytochrome C reductase iron-sulfur subunit

Ubiquinol-cytochrome C reductase complex 17 kDa protein

Ubiquinol-cytochrome C reductase complex 14 kDa protein

Ubiquinol-cytochrome C reductase complex ubiquinone-binding protein QP-C

Ubiquinol-cytochrome C reductase complex 7.3 kDa protein

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