SMTL ID : 1ntk.1

Crystal Structure of Mitochondrial Cytochrome bc1 in Complex with Antimycin A1

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.60 Å

Oligo State

hetero-oligomer

Ligands

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

HEM.1: 21 residues within 4Å: Chain C: Q.44, I.45, G.48, L.49, L.51, Y.55, R.80, H.83, A.84, A.87, T.126, A.127, G.130, Y.131, L.133, P.134, F.179, H.182, F.183, P.186, F.187 16 PLIP interactions: 16 interactions with chain C, Hydrophobic interactions: C:Q.44, C:I.45, C:L.51, C:Y.55, C:T.126, C:A.127, C:Y.131, C:L.133, C:L.133, C:F.179, C:F.187 Salt bridges: C:R.80, C:R.80 pi-Cation interactions: C:H.182 Metal complexes: C:H.83, C:H.182 HEM.2: 18 residues within 4Å: Chain C: W.31, G.34, L.37, L.94, H.97, V.98, R.100, S.106, F.109, T.112, W.113, G.116, V.117, L.119, H.196, L.200, N.206 Ligands: AY1.3 19 PLIP interactions: 19 interactions with chain C, Hydrophobic interactions: C:L.37, C:L.37, C:V.98, C:T.112, C:W.113, C:W.113, C:V.117, C:L.119, C:L.119, C:L.200 Hydrogen bonds: C:G.34, C:S.106, C:N.206 Salt bridges: C:H.97, C:R.100, C:R.100 pi-Stacking: C:H.97 Metal complexes: C:H.97, C:H.196 HEM.4: 21 residues within 4Å: Chain D: C.37, C.40, H.41, N.105, A.108, L.109, P.110, P.111, I.116, R.120, Y.126, V.127, L.130, L.131, F.153, I.158, G.159, M.160, A.161, P.163, V.186 13 PLIP interactions: 13 interactions with chain D, Hydrophobic interactions: D:N.105, D:I.116, D:V.127, D:L.130, D:F.153, D:M.160, D:A.161, D:P.163, D:V.186 Hydrogen bonds: D:Y.126, D:G.159 Salt bridges: D:R.120 Metal complexes: D:H.41 HEM.6: 21 residues within 4Å: Chain N: Q.44, I.45, G.48, L.49, L.51, Y.55, R.80, H.83, A.84, A.87, T.126, A.127, G.130, Y.131, L.133, P.134, F.179, H.182, F.183, P.186, F.187 16 PLIP interactions: 16 interactions with chain N, Hydrophobic interactions: N:Q.44, N:I.45, N:L.51, N:Y.55, N:T.126, N:A.127, N:Y.131, N:L.133, N:L.133, N:F.179, N:F.187 Salt bridges: N:R.80, N:R.80 pi-Cation interactions: N:H.182 Metal complexes: N:H.83, N:H.182 HEM.7: 18 residues within 4Å: Chain N: W.31, G.34, L.37, L.94, H.97, V.98, R.100, S.106, F.109, T.112, W.113, G.116, V.117, L.119, H.196, L.200, N.206 Ligands: AY1.8 19 PLIP interactions: 19 interactions with chain N, Hydrophobic interactions: N:L.37, N:L.37, N:V.98, N:T.112, N:W.113, N:W.113, N:V.117, N:L.119, N:L.119, N:L.200 Hydrogen bonds: N:G.34, N:S.106, N:N.206 Salt bridges: N:H.97, N:R.100, N:R.100 pi-Stacking: N:H.97 Metal complexes: N:H.97, N:H.196 HEM.9: 21 residues within 4Å: Chain O: C.37, C.40, H.41, N.105, A.108, L.109, P.110, P.111, I.116, R.120, Y.126, V.127, L.130, L.131, F.153, I.158, G.159, M.160, A.161, P.163, V.186 13 PLIP interactions: 13 interactions with chain O, Hydrophobic interactions: O:N.105, O:I.116, O:V.127, O:L.130, O:F.153, O:M.160, O:A.161, O:P.163, O:V.186 Hydrogen bonds: O:Y.126, O:G.159 Salt bridges: O:R.120 Metal complexes: O:H.41

2 x AY1: [(2R,3S,6S,7R,8R)-3-[(3-FORMAMIDO-2-OXIDANYL-PHENYL)CARBONYLAMINO]-8-HEXYL-2,6-DIMETHYL-4,9-BIS(OXIDANYLIDENE)-1,5-DIOXONAN-7-YL] 2-METHYLPROPANOATE(Non-covalent)

AY1.3: 13 residues within 4Å: Chain C: F.18, I.27, W.31, G.34, S.35, G.38, M.190, L.197, F.220, Y.224, K.227, D.228 Ligands: HEM.2 6 PLIP interactions: 6 interactions with chain C Hydrophobic interactions: C:F.18, C:F.18, C:I.27 Hydrogen bonds: C:K.227, C:D.228 pi-Stacking: C:F.220 AY1.8: 13 residues within 4Å: Chain N: F.18, I.27, W.31, G.34, S.35, G.38, M.190, L.197, F.220, Y.224, K.227, D.228 Ligands: HEM.7 6 PLIP interactions: 6 interactions with chain N Hydrophobic interactions: N:F.18, N:F.18, N:I.27 Hydrogen bonds: N:K.227, N:D.228 pi-Stacking: N:F.220

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

FES.5: 9 residues within 4Å: Chain E: C.139, H.141, L.142, C.144, C.158, C.160, H.161, G.162, S.163 4 PLIP interactions: 4 interactions with chain E, Metal complexes: E:C.139, E:H.141, E:C.158, E:H.161 FES.10: 9 residues within 4Å: Chain P: C.139, H.141, L.142, C.144, C.158, C.160, H.161, G.162, S.163 4 PLIP interactions: 4 interactions with chain P, Metal complexes: P:C.139, P:H.141, P:C.158, P:H.161

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Gao, X. et al., Structural basis for the quinone reduction in the bc(1) complex: a comparative analysis of crystal structures of mitochondrial cytochrome bc(1) with bound substrate and inhibitors at the Q(i) site. Biochemistry (2003)

Release Date

2003-10-07

Peptides

Ubiquinol-cytochrome C reductase complex core protein I, mitochondrial: AL
Ubiquinol-cytochrome C reductase complex core protein 2, mitochondrial: BM
Cytochrome b: CN
cytochrome c1: DO
UBIQUINOL-CYTOCHROME C REDUCTASE IRON-SULFUR SUBUNIT, MITOCHONDRIAL: EP
Ubiquinol-cytochrome C reductase complex 14 kDa protein: FQ
Ubiquinol-cytochrome C reductase complex ubiquinone-binding protein QP-C: GR
Ubiquinol-cytochrome C reductase complex 11 kDa protein: HS
Ubiquinol-cytochrome C reductase 8 kDa protein: IT
Ubiquinol-cytochrome C reductase complex 7.2 kDa protein: JU
Ubiquinol-cytochrome C reductase complex 6.4 kDa protein: KV

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

L
A

B
B

M
B

C
C

N
C

D
D

O
D

E
E

P
E

F
F

Q
F

G
G

R
G

H
H

S
H

I
I

T
I

J
J

U
J

K
K

V
K

Membrane

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

Ubiquinol-cytochrome C reductase complex core protein 2, mitochondrial

Cytochrome b

cytochrome c1

UBIQUINOL-CYTOCHROME C REDUCTASE IRON-SULFUR SUBUNIT, MITOCHONDRIAL

Ubiquinol-cytochrome C reductase complex 14 kDa protein

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

Ubiquinol-cytochrome C reductase complex 11 kDa protein

Ubiquinol-cytochrome C reductase 8 kDa protein

Ubiquinol-cytochrome C reductase complex 7.2 kDa protein

Ubiquinol-cytochrome C reductase complex 6.4 kDa protein

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