SMTL ID : 1sqx.1

Crystal Structure Analysis of Bovine Bc1 with Stigmatellin A

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.60 Å

Oligo State

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

Ligands

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

UQ2.1: 14 residues within 4Å: Chain C: F.18, L.21, W.31, S.35, G.38, M.190, A.193, L.197, L.200, H.201, S.205, F.220, D.228 Ligands: HEC.2 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:A.193, C:L.197 UQ2.7: 14 residues within 4Å: Chain N: F.18, L.21, W.31, S.35, G.38, M.190, A.193, L.197, L.200, H.201, S.205, F.220, D.228 Ligands: HEC.8 2 PLIP interactions: 2 interactions with chain N Hydrophobic interactions: N:A.193, N:L.197

6 x HEC: HEME C(Non-covalent)

HEC.2: 23 residues within 4Å: Chain C: W.31, G.34, S.35, L.37, G.38, L.94, H.97, V.98, R.100, S.106, F.109, T.112, W.113, G.116, V.117, L.119, L.120, H.196, L.197, L.200, S.205, N.206 Ligands: UQ2.1 19 PLIP interactions: 19 interactions with chain C, Hydrophobic interactions: C:L.37, C:L.37, C:L.94, C:T.112, C:V.117, C:L.119, C:L.120, C:L.197, C:L.200, C:L.200 Hydrogen bonds: C:G.34, C:S.106, C:N.206 Water bridges: C:F.33 Salt bridges: C:H.97, C:R.100, C:R.100 Metal complexes: C:H.97, C:H.196 HEC.3: 20 residues within 4Å: Chain C: Q.44, I.45, G.48, L.49, Y.55, V.66, R.80, H.83, A.87, T.126, A.127, G.130, Y.131, L.133, P.134, F.179, H.182, F.183, P.186, Y.273 15 PLIP interactions: 15 interactions with chain C, Hydrophobic interactions: C:Q.44, C:Y.55, C:V.66, C:A.87, C:T.126, C:L.133, C:L.133, C:F.179, C:F.183, C:F.183, C:P.186 Salt bridges: C:R.80, C:R.80 Metal complexes: C:H.83, C:H.182 HEC.6: 21 residues within 4Å: Chain E: V.36, C.37, C.40, H.41, N.105, A.108, L.109, P.110, P.111, I.116, R.120, Y.126, L.130, L.131, F.153, I.158, G.159, M.160, A.161, P.163, I.164 13 PLIP interactions: 13 interactions with chain E, Hydrophobic interactions: E:A.108, E:P.110, E:I.116, E:L.130, E:L.131, E:F.153, E:I.158, E:A.161, E:P.163, E:I.164 Hydrogen bonds: E:G.159 Salt bridges: E:R.120 Metal complexes: E:H.41 HEC.8: 23 residues within 4Å: Chain N: W.31, G.34, S.35, L.37, G.38, L.94, H.97, V.98, R.100, S.106, F.109, T.112, W.113, G.116, V.117, L.119, L.120, H.196, L.197, L.200, S.205, N.206 Ligands: UQ2.7 19 PLIP interactions: 19 interactions with chain N, Hydrophobic interactions: N:L.37, N:L.37, N:L.94, N:T.112, N:V.117, N:L.119, N:L.120, N:L.197, N:L.200, N:L.200 Hydrogen bonds: N:G.34, N:S.106, N:N.206 Water bridges: N:F.33 Salt bridges: N:H.97, N:R.100, N:R.100 Metal complexes: N:H.97, N:H.196 HEC.9: 20 residues within 4Å: Chain N: Q.44, I.45, G.48, L.49, Y.55, V.66, R.80, H.83, A.87, T.126, A.127, G.130, Y.131, L.133, P.134, F.179, H.182, F.183, P.186, Y.273 15 PLIP interactions: 15 interactions with chain N, Hydrophobic interactions: N:Q.44, N:Y.55, N:V.66, N:A.87, N:T.126, N:L.133, N:L.133, N:F.179, N:F.183, N:F.183, N:P.186 Salt bridges: N:R.80, N:R.80 Metal complexes: N:H.83, N:H.182 HEC.12: 21 residues within 4Å: Chain P: V.36, C.37, C.40, H.41, N.105, A.108, L.109, P.110, P.111, I.116, R.120, Y.126, L.130, L.131, F.153, I.158, G.159, M.160, A.161, P.163, I.164 13 PLIP interactions: 13 interactions with chain P, Hydrophobic interactions: P:A.108, P:P.110, P:I.116, P:L.130, P:L.131, P:F.153, P:I.158, P:A.161, P:P.163, P:I.164 Hydrogen bonds: P:G.159 Salt bridges: P:R.120 Metal complexes: P:H.41

2 x SMA: STIGMATELLIN A(Non-covalent)

SMA.4: 20 residues within 4Å: Chain C: L.121, M.124, A.125, F.128, M.129, M.138, G.142, V.145, I.146, I.164, I.268, K.269, P.270, E.271, F.274, Y.278, L.294, I.298 Chain O: C.160, H.161 8 PLIP interactions: 8 interactions with chain C Hydrophobic interactions: C:F.128, C:I.146, C:I.164, C:P.270, C:F.274, C:F.274, C:L.294 Hydrogen bonds: C:E.271 SMA.10: 20 residues within 4Å: Chain D: C.160, H.161 Chain N: L.121, M.124, A.125, F.128, M.129, M.138, G.142, V.145, I.146, I.164, I.268, K.269, P.270, E.271, F.274, Y.278, L.294, I.298 8 PLIP interactions: 8 interactions with chain N Hydrophobic interactions: N:F.128, N:I.146, N:I.164, N:P.270, N:F.274, N:F.274, N:L.294 Hydrogen bonds: N:E.271

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

FES.5: 10 residues within 4Å: Chain D: 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 D, Metal complexes: D:C.139, D:H.141, D:C.158, D:H.161 FES.11: 10 residues within 4Å: Chain O: 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 O, Metal complexes: O:C.139, O:H.141, O:C.158, O: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 precursor: AL
Ubiquinol-cytochrome-c reductase complex core protein 2, mitochondrial precursor: BM
Cytochrome b: CN
Cytochrome c1, heme protein, mitochondrial: DO
Ubiquinol-cytochrome c reductase iron-sulfur subunit, mitochondrial precursor (EC 1.10.2.2) (Rieske iron-sulfur protein) (RISP) [Contains: Ubiquinol-cytochrome c reductase 8 kDa protein (Complex III subunit IX)]: 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 iron-sulfur subunit, mitochondrial precursor (EC 1.10.2.2) (Rieske iron-sulfur protein) (RISP) [Contains: Ubiquinol-cytochrome c reductase 8 kDa protein (Complex III subunit IX)]: 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
E

O
E

E
D

P
D

F
G

Q
G

G
I

R
I

H
F

S
F

I
K

T
K

J
H

U
H

K
J

V
J

Membrane

We predict this structure to be a membrane protein.
Show / Hide

Ubiquinol-cytochrome-c reductase complex core protein I, mitochondrial precursor

Ubiquinol-cytochrome-c reductase complex core protein 2, mitochondrial precursor

Cytochrome b

Cytochrome c1, heme protein, mitochondrial

Ubiquinol-cytochrome c reductase iron-sulfur subunit, mitochondrial precursor (EC 1.10.2.2) (Rieske iron-sulfur protein) (RISP) [Contains: Ubiquinol-cytochrome c reductase 8 kDa protein (Complex III subunit IX)]

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 iron-sulfur subunit, mitochondrial precursor (EC 1.10.2.2) (Rieske iron-sulfur protein) (RISP) [Contains: Ubiquinol-cytochrome c reductase 8 kDa protein (Complex III subunit IX)]

Ubiquinol-cytochrome C reductase complex 7.2 kDa protein

Ubiquinol-cytochrome C reductase complex 6.4 kDa protein

Related Entries With Identical Sequence