SMTL ID : 1sqb.1

Crystal Structure Analysis of Bovine Bc1 with Azoxystrobin

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.69 Å

Oligo State

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

Ligands

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

HEM.1: 19 residues within 4Å: Chain C: W.31, G.34, L.37, G.38, L.94, H.97, V.98, R.100, S.106, W.113, G.116, V.117, L.119, L.120, H.196, L.197, L.200, S.205, N.206 19 PLIP interactions: 19 interactions with chain C, Hydrophobic interactions: C:L.37, C:L.37, C:L.94, C:V.117, C:L.119, C:L.119, C:L.120, C:L.197, C:L.200, C:L.200 Hydrogen bonds: C:G.34, C:S.205, C:N.206, C:N.206 Salt bridges: C:H.97, C:R.100, C:R.100 Metal complexes: C:H.97, C:H.196 HEM.2: 23 residues within 4Å: Chain C: L.41, 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, I.189, Y.273 18 PLIP interactions: 18 interactions with chain C, Hydrophobic interactions: C:L.41, C:Q.44, C:I.45, C:L.49, C:L.51, C:Y.55, C:A.84, C:T.126, C:L.133, C:L.133, C:F.179, C:F.183, C:F.183, C:I.189 Salt bridges: C:R.80, C:R.80 Metal complexes: C:H.83, C:H.182 HEM.4: 20 residues within 4Å: Chain D: V.36, C.37, C.40, H.41, N.105, N.106, A.108, L.109, P.110, P.111, R.120, Y.126, V.127, L.130, L.131, F.153, I.158, G.159, M.160, P.163 12 PLIP interactions: 12 interactions with chain D, Hydrophobic interactions: D:V.36, D:N.105, D:A.108, D:P.110, D:P.111, D:V.127, D:L.130, D:L.131, D:P.163 Hydrogen bonds: D:G.159 Salt bridges: D:R.120 Metal complexes: D:H.41 HEM.6: 19 residues within 4Å: Chain N: W.31, G.34, L.37, G.38, L.94, H.97, V.98, R.100, S.106, W.113, G.116, V.117, L.119, L.120, H.196, L.197, L.200, S.205, N.206 19 PLIP interactions: 19 interactions with chain N, Hydrophobic interactions: N:L.37, N:L.37, N:L.94, N:V.117, N:L.119, N:L.119, N:L.120, N:L.197, N:L.200, N:L.200 Hydrogen bonds: N:G.34, N:S.205, N:N.206, N:N.206 Salt bridges: N:H.97, N:R.100, N:R.100 Metal complexes: N:H.97, N:H.196 HEM.7: 23 residues within 4Å: Chain N: L.41, 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, I.189, Y.273 18 PLIP interactions: 18 interactions with chain N, Hydrophobic interactions: N:L.41, N:Q.44, N:I.45, N:L.49, N:L.51, N:Y.55, N:A.84, N:T.126, N:L.133, N:L.133, N:F.179, N:F.183, N:F.183, N:I.189 Salt bridges: N:R.80, N:R.80 Metal complexes: N:H.83, N:H.182 HEM.9: 20 residues within 4Å: Chain O: V.36, C.37, C.40, H.41, N.105, N.106, A.108, L.109, P.110, P.111, R.120, Y.126, V.127, L.130, L.131, F.153, I.158, G.159, M.160, P.163 12 PLIP interactions: 12 interactions with chain O, Hydrophobic interactions: O:V.36, O:N.105, O:A.108, O:P.110, O:P.111, O:V.127, O:L.130, O:L.131, O:P.163 Hydrogen bonds: O:G.159 Salt bridges: O:R.120 Metal complexes: O:H.41

2 x AZO: METHYL (2Z)-2-(2-{[6-(2-CYANOPHENOXY)PYRIMIDIN-4-YL]OXY}PHENYL)-3-METHOXYACRYLATE(Non-covalent)

AZO.3: 19 residues within 4Å: Chain C: M.124, A.127, F.128, Y.131, V.132, M.138, S.139, G.142, A.143, I.146, K.269, P.270, E.271, Y.273, F.274, A.277, Y.278, L.294, I.298 9 PLIP interactions: 9 interactions with chain C Hydrophobic interactions: C:F.128, C:Y.131, C:P.270, C:F.274, C:A.277, C:L.294, C:L.294, C:I.298 pi-Stacking: C:F.274 AZO.8: 19 residues within 4Å: Chain N: M.124, A.127, F.128, Y.131, V.132, M.138, S.139, G.142, A.143, I.146, K.269, P.270, E.271, Y.273, F.274, A.277, Y.278, L.294, I.298 9 PLIP interactions: 9 interactions with chain N Hydrophobic interactions: N:F.128, N:Y.131, N:P.270, N:F.274, N:A.277, N:L.294, N:L.294, N:I.298 pi-Stacking: N:F.274

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

FES.5: 10 residues within 4Å: Chain E: C.139, H.141, L.142, G.143, C.144, C.158, C.160, H.161, G.162, S.163 1 PLIP interactions: 1 interactions with chain E, Metal complexes: E:C.158 FES.10: 10 residues within 4Å: Chain P: C.139, H.141, L.142, G.143, C.144, C.158, C.160, H.161, G.162, S.163 1 PLIP interactions: 1 interactions with chain P, Metal complexes: P:C.158

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Esser, L. et al., Crystallographic studies of quinol oxidation site inhibitors: a modified classification of inhibitors for the cytochrome bc(1) complex. J.Mol.Biol. (2004)

Release Date

2004-09-07

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, heme protein, mitochondrial: DO
Ubiquinol-cytochrome c reductase iron-sulfur subunit: 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, heme protein, mitochondrial

Ubiquinol-cytochrome c reductase iron-sulfur subunit

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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