SMTL ID : 1sqv.1

Crystal Structure Analysis of Bovine Bc1 with UHDBT

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.85 Å

Oligo State

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

Ligands

6 x HEC: HEME C(Non-covalent)

HEC.1: 24 residues within 4Å: Chain C: Q.44, I.45, G.48, L.49, L.51, A.52, Y.55, R.80, H.83, A.84, A.87, F.90, T.126, A.127, G.130, Y.131, L.133, P.134, F.179, H.182, F.183, P.186, F.187, Y.273 16 PLIP interactions: 16 interactions with chain C, Hydrophobic interactions: C:Q.44, C:Q.44, C:I.45, C:L.51, C:Y.55, C:A.84, C:F.90, C:T.126, C:L.133, C:F.179, C:F.183, C:F.187 Salt bridges: C:R.80, C:R.80 Metal complexes: C:H.83, C:H.182 HEC.2: 19 residues within 4Å: Chain C: W.31, G.34, L.37, G.38, H.97, V.98, R.100, S.106, F.109, W.113, G.116, V.117, L.119, L.120, H.196, L.200, S.205, N.206 Ligands: UQ2.4 17 PLIP interactions: 17 interactions with chain C, Hydrophobic interactions: C:L.37, C:L.37, C:L.37, C:V.98, C:V.117, C:L.120, C:L.200, C:L.200 Hydrogen bonds: C:G.34, C:S.106, C:S.205, C:N.206 Salt bridges: C:H.97, C:R.100, C:R.100 Metal complexes: C:H.97, C:H.196 HEC.5: 18 residues within 4Å: Chain D: C.37, C.40, H.41, N.105, A.108, L.109, P.110, P.111, R.120, Y.126, L.131, F.153, I.158, G.159, M.160, A.161, P.163, I.164 8 PLIP interactions: 8 interactions with chain D, Hydrophobic interactions: D:N.105, D:P.110, D:L.131, D:F.153, D:A.161, D:I.164 Salt bridges: D:R.120 Metal complexes: D:H.41 HEC.7: 24 residues within 4Å: Chain N: Q.44, I.45, G.48, L.49, L.51, A.52, Y.55, R.80, H.83, A.84, A.87, F.90, T.126, A.127, G.130, Y.131, L.133, P.134, F.179, H.182, F.183, P.186, F.187, Y.273 16 PLIP interactions: 16 interactions with chain N, Hydrophobic interactions: N:Q.44, N:Q.44, N:I.45, N:L.51, N:Y.55, N:A.84, N:F.90, N:T.126, N:L.133, N:F.179, N:F.183, N:F.187 Salt bridges: N:R.80, N:R.80 Metal complexes: N:H.83, N:H.182 HEC.8: 19 residues within 4Å: Chain N: W.31, G.34, L.37, G.38, H.97, V.98, R.100, S.106, F.109, W.113, G.116, V.117, L.119, L.120, H.196, L.200, S.205, N.206 Ligands: UQ2.10 17 PLIP interactions: 17 interactions with chain N, Hydrophobic interactions: N:L.37, N:L.37, N:L.37, N:V.98, N:V.117, N:L.120, N:L.200, N:L.200 Hydrogen bonds: N:G.34, N:S.106, N:S.205, N:N.206 Salt bridges: N:H.97, N:R.100, N:R.100 Metal complexes: N:H.97, N:H.196 HEC.11: 18 residues within 4Å: Chain O: C.37, C.40, H.41, N.105, A.108, L.109, P.110, P.111, R.120, Y.126, L.131, F.153, I.158, G.159, M.160, A.161, P.163, I.164 8 PLIP interactions: 8 interactions with chain O, Hydrophobic interactions: O:N.105, O:P.110, O:L.131, O:F.153, O:A.161, O:I.164 Salt bridges: O:R.120 Metal complexes: O:H.41

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

UHD.3: 16 residues within 4Å: Chain C: L.121, M.124, A.125, Y.131, M.138, W.141, G.142, V.145, I.146, I.268, K.269, P.270, F.274, Y.278, L.281 Chain P: H.161 7 PLIP interactions: 7 interactions with chain C Hydrophobic interactions: C:L.121, C:A.125, C:I.146, C:I.146, C:F.274, C:F.274 Hydrogen bonds: C:Y.278 UHD.9: 16 residues within 4Å: Chain E: H.161 Chain N: L.121, M.124, A.125, Y.131, M.138, W.141, G.142, V.145, I.146, I.268, K.269, P.270, F.274, Y.278, L.281 7 PLIP interactions: 7 interactions with chain N Hydrophobic interactions: N:L.121, N:A.125, N:I.146, N:I.146, N:F.274, N:F.274 Hydrogen bonds: N:Y.278

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

UQ2.4: 14 residues within 4Å: Chain C: F.18, A.23, I.27, W.31, S.35, G.38, M.190, L.197, L.200, H.201, S.205, F.220, D.228 Ligands: HEC.2 5 PLIP interactions: 5 interactions with chain C Hydrophobic interactions: C:F.18, C:L.197, C:F.220 Hydrogen bonds: C:S.205 Water bridges: C:S.35 UQ2.10: 14 residues within 4Å: Chain N: F.18, A.23, I.27, W.31, S.35, G.38, M.190, L.197, L.200, H.201, S.205, F.220, D.228 Ligands: HEC.8 5 PLIP interactions: 5 interactions with chain N Hydrophobic interactions: N:F.18, N:L.197, N:F.220 Hydrogen bonds: N:S.205 Water bridges: N:S.35

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

FES.6: 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 4 PLIP interactions: 4 interactions with chain E, Metal complexes: E:C.139, E:H.141, E:C.158, E:H.161 FES.12: 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 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

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

2005-09-06

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 complex 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 complex 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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