SMTL ID : 2fyu.1

Crystal structure of bovine heart mitochondrial bc1 with jg144 inhibitor

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.26 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: 23 residues within 4Å: Chain C: Q.44, I.45, G.48, L.49, L.51, A.52, Y.55, V.66, R.80, H.83, 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 19 PLIP interactions: 19 interactions with chain C, Hydrophobic interactions: C:Q.44, C:Q.44, C:I.45, C:L.51, C:Y.55, C:Y.55, C:V.66, C:F.90, C:T.126, C:A.127, C:L.133, 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 HEM.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, I.189, H.196, L.197, L.200, S.205, N.206 24 PLIP interactions: 24 interactions with chain C, Hydrophobic interactions: C:L.37, C:T.112, C:W.113, C:W.113, C:V.117, C:L.119, C:L.119, C:L.120, C:I.189, C:L.197, C:L.200, C:L.200 Hydrogen bonds: C:G.34, C:S.106, C:S.205, C:N.206 Water bridges: C:N.32, C:F.33, C:S.35 Salt bridges: C:H.97, C:R.100, C:R.100 Metal complexes: C:H.97, C:H.196 HEM.4: 20 residues within 4Å: Chain D: 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, P.163, I.164 13 PLIP interactions: 13 interactions with chain D, Hydrophobic interactions: D:N.105, D:P.110, D:I.116, D:L.130, D:L.131, D:F.153, D:I.158, D:M.160, D:I.164 Hydrogen bonds: D:Y.126, D:G.159 Salt bridges: D:R.120 Metal complexes: D:H.41 HEM.6: 23 residues within 4Å: Chain N: Q.44, I.45, G.48, L.49, L.51, A.52, Y.55, V.66, R.80, H.83, 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 19 PLIP interactions: 19 interactions with chain N, Hydrophobic interactions: N:Q.44, N:Q.44, N:I.45, N:L.51, N:Y.55, N:Y.55, N:V.66, N:F.90, N:T.126, N:A.127, N:L.133, 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 HEM.7: 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, I.189, H.196, L.197, L.200, S.205, N.206 24 PLIP interactions: 24 interactions with chain N, Hydrophobic interactions: N:L.37, N:T.112, N:W.113, N:W.113, N:V.117, N:L.119, N:L.119, N:L.120, N:I.189, N:L.197, N:L.200, N:L.200 Hydrogen bonds: N:G.34, N:S.106, N:S.205, N:N.206 Water bridges: N:N.32, N:F.33, N:S.35 Salt bridges: N:H.97, N:R.100, N:R.100 Metal complexes: N:H.97, N:H.196 HEM.9: 20 residues within 4Å: Chain O: 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, P.163, I.164 13 PLIP interactions: 13 interactions with chain O, Hydrophobic interactions: O:N.105, O:P.110, O:I.116, O:L.130, O:L.131, O:F.153, O:I.158, O:M.160, O:I.164 Hydrogen bonds: O:Y.126, O:G.159 Salt bridges: O:R.120 Metal complexes: O:H.41

2 x FDN: (5S)-3-ANILINO-5-(2,4-DIFLUOROPHENYL)-5-METHYL-1,3-OXAZOLIDINE-2,4-DIONE(Non-covalent)

FDN.3: 16 residues within 4Å: Chain C: M.124, A.127, F.128, Y.131, M.138, G.142, A.143, V.145, I.146, I.268, K.269, P.270, E.271, Y.273, F.274, Y.278 12 PLIP interactions: 12 interactions with chain C Hydrophobic interactions: C:F.128, C:Y.131, C:V.145, C:I.146, C:I.146, C:I.268, C:P.270, C:E.271, C:Y.273, C:F.274, C:Y.278 Hydrogen bonds: C:E.271 FDN.8: 16 residues within 4Å: Chain N: M.124, A.127, F.128, Y.131, M.138, G.142, A.143, V.145, I.146, I.268, K.269, P.270, E.271, Y.273, F.274, Y.278 12 PLIP interactions: 12 interactions with chain N Hydrophobic interactions: N:F.128, N:Y.131, N:V.145, N:I.146, N:I.146, N:I.268, N:P.270, N:E.271, N:Y.273, N:F.274, N:Y.278 Hydrogen bonds: N:E.271

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 4 PLIP interactions: 4 interactions with chain E, Metal complexes: E:C.139, E:H.141, E:C.158, E:H.161 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 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., Surface-modulated motion switch: Capture and release of iron-sulfur protein in the cytochrome bc1 complex. Proc.Natl.Acad.Sci.Usa (2006)

Release Date

2006-08-29

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, mitochondrial: EP
Hypothetical protein LOC616871: 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: 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, mitochondrial

Hypothetical protein LOC616871

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

Ubiquinol-cytochrome c reductase complex 7.2 kDa protein

Ubiquinol-cytochrome c reductase complex 6.4 kDa protein

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