SMTL ID : 2ibz.1

Yeast Cytochrome BC1 Complex with Stigmatellin

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

hetero-1-1-1-1-1-1-1-1-1-1-1-mer

Ligands

3 x HEC: HEME C(Non-covalent)(Covalent)

HEC.1: 20 residues within 4Å: Chain C: L.40, Q.43, G.47, I.48, M.50, A.51, R.79, H.82, A.83, A.86, F.89, T.127, A.128, G.131, Y.132, V.135, H.183, Y.184, P.187, Y.274 15 PLIP interactions: 15 interactions with chain C, Hydrophobic interactions: C:L.40, C:Q.43, C:A.51, C:A.83, C:F.89, C:F.89, C:T.127, C:Y.184 Salt bridges: C:R.79, C:R.79 pi-Stacking: C:H.82, C:H.183 pi-Cation interactions: C:H.183 Metal complexes: C:H.82, C:H.183 HEC.2: 23 residues within 4Å: Chain C: W.30, G.33, L.36, G.37, F.89, M.93, H.96, M.97, K.99, S.105, L.113, W.114, G.117, V.118, I.120, F.121, V.194, H.197, L.198, L.201, S.206, S.207 Ligands: UQ6.3 26 PLIP interactions: 26 interactions with chain C, Hydrophobic interactions: C:L.36, C:L.36, C:F.89, C:L.113, C:L.113, C:W.114, C:W.114, C:V.118, C:I.120, C:F.121, C:V.194, C:V.194, C:L.198, C:L.201 Hydrogen bonds: C:W.30, C:G.33, C:S.105, C:S.207 Water bridges: C:M.32, C:M.32, C:S.34 Salt bridges: C:H.96, C:K.99, C:K.99 Metal complexes: C:H.96, C:H.197 HEC.5: 19 residues within 4Å: Chain D: V.39, C.40, C.43, H.44, N.108, P.113, P.114, I.119, R.123, Y.129, I.130, L.134, F.157, I.162, A.163, M.164, V.167, L.168, L.194 16 PLIP interactions: 16 interactions with chain D, Hydrophobic interactions: D:P.113, D:P.114, D:I.119, D:I.130, D:L.134, D:L.134, D:I.162, D:M.164, D:V.167, D:L.168, D:L.194 Hydrogen bonds: D:Y.129, D:A.163 Salt bridges: D:R.123 pi-Stacking: D:H.44 Metal complexes: D:H.44

1 x UQ6: 5-(3,7,11,15,19,23-HEXAMETHYL-TETRACOSA-2,6,10,14,18,22-HEXAENYL)-2,3-DIMETHOXY-6-METHYL-BENZENE-1,4-DIOL(Non-covalent)

UQ6.3: 10 residues within 4Å: Chain C: Y.16, Q.22, S.34, I.44, F.49, L.201, S.206, M.221, D.229 Ligands: HEC.2 4 PLIP interactions: 4 interactions with chain C Hydrophobic interactions: C:I.44, C:F.49 Hydrogen bonds: C:Q.22 Water bridges: C:S.20

1 x SMA: STIGMATELLIN A(Non-covalent)

SMA.4: 17 residues within 4Å: Chain C: T.122, I.125, M.139, G.143, V.146, I.147, F.151, I.269, V.270, P.271, E.272, L.275, F.278, Y.279, M.295, F.296, I.299 7 PLIP interactions: 7 interactions with chain C Hydrophobic interactions: C:I.125, C:V.146, C:F.151, C:P.271, C:L.275, C:F.278 Hydrogen bonds: C:E.272

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

FES.6: 10 residues within 4Å: Chain E: C.129, H.131, L.132, G.133, C.134, C.148, C.150, H.151, G.152, S.153 4 PLIP interactions: 4 interactions with chain E, Metal complexes: E:C.129, E:H.131, E:C.148, E:H.151

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Lancaster, C.R. et al., A Comparison of Stigmatellin Conformations, Free and Bound to the Photosynthetic Reaction Center and the Cytochrome bc(1) Complex. J.Mol.Biol. (2007)

Release Date

2007-03-20

Peptides

Ubiquinol-cytochrome-c reductase complex core protein 1: A
Ubiquinol-cytochrome-c reductase complex core protein 2: B
Cytochrome b: C
Cytochrome c1, heme protein, mitochondrial precursor: D
Ubiquinol-cytochrome c reductase iron-sulfur subunit, mitochondrial precursor: E
Ubiquinol-cytochrome c reductase complex 17 kDa protein: F
Ubiquinol-cytochrome c reductase complex 14 kDa protein: G
Ubiquinol-cytochrome c reductase complex ubiquinone-binding protein QP-C: H
Ubiquinol-cytochrome c reductase complex 7.3 kDa protein: I
Variable Heavy chain of antibody fragment: J
Variable Light chain of antibody fragment: K

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
H

G
F

H
G

I
I

J
X

K
Y

Membrane

We predict this structure to be a membrane protein.
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Ubiquinol-cytochrome-c reductase complex core protein 1

Ubiquinol-cytochrome-c reductase complex core protein 2

Cytochrome b

Cytochrome c1, heme protein, mitochondrial precursor

Ubiquinol-cytochrome c reductase iron-sulfur subunit, mitochondrial precursor

Ubiquinol-cytochrome c reductase complex 17 kDa protein

Ubiquinol-cytochrome c reductase complex 14 kDa protein

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

Ubiquinol-cytochrome c reductase complex 7.3 kDa protein

Variable Heavy chain of antibody fragment

Variable Light chain of antibody fragment

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