SMTL ID : 1kb9.1

YEAST CYTOCHROME BC1 COMPLEX

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

1 x PCF: 1,2-DIACYL-SN-GLYCERO-3-PHOSHOCHOLINE(Non-covalent)

PCF.1: 10 residues within 4Å: Chain A: S.424 Chain C: H.222, I.226, F.227 Chain D: K.230 Chain E: V.30, M.33, S.37 Ligands: UMQ.2, PIE.7 5 PLIP interactions: 4 interactions with chain C, 1 interactions with chain A Hydrophobic interactions: C:I.226, C:F.227 Salt bridges: C:H.222, C:H.222 Hydrogen bonds: A:S.424

1 x UMQ: UNDECYL-MALTOSIDE(Non-covalent)

UMQ.2: 16 residues within 4Å: Chain A: W.401, D.402, S.427, M.428, M.429, R.430 Chain E: Y.27, V.30, S.38 Chain I: N.11, A.12, V.13, F.14, V.15, I.18 Ligands: PCF.1 9 PLIP interactions: 4 interactions with chain A, 4 interactions with chain I, 1 interactions with chain E Hydrogen bonds: A:S.427, A:M.428, A:R.430, A:R.430, I:A.12, I:V.15, E:Y.27 Hydrophobic interactions: I:V.15, I:I.18

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

HEM.3: 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.82, C:H.183 Metal complexes: C:H.82, C:H.183 HEM.4: 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: UQ6.6 27 PLIP interactions: 27 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, C:R.110 Metal complexes: C:H.96, C:H.197 HEM.11: 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 17 PLIP interactions: 17 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 pi-Cation interactions: D:H.44 Metal complexes: D:H.44

1 x SMA: STIGMATELLIN A(Non-covalent)

SMA.5: 19 residues within 4Å: Chain C: T.122, I.125, A.126, F.129, M.139, G.143, V.146, I.147, F.151, L.165, I.269, V.270, P.271, E.272, L.275, F.278, Y.279, M.295, F.296 11 PLIP interactions: 11 interactions with chain C Hydrophobic interactions: C:I.125, C:F.129, C:F.129, C:V.146, C:I.147, C:I.147, C:F.151, C:L.165, C:P.271, C:F.278 Hydrogen bonds: C:E.272

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)

UQ6.6: 11 residues within 4Å: Chain C: Y.16, Q.22, W.30, G.37, L.40, I.44, L.201, S.206, M.221, D.229 Ligands: HEM.4 4 PLIP interactions: 4 interactions with chain C Hydrophobic interactions: C:L.40, C:I.44 Hydrogen bonds: C:Q.22 Water bridges: C:S.20

1 x PIE: 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOINOSITOL(Non-covalent)

PIE.7: 17 residues within 4Å: Chain C: N.74, M.237, F.245 Chain D: L.208, K.211, T.212, I.215, L.216 Chain E: S.37, G.40, A.41, S.43, T.44, E.46, T.47, S.50 Ligands: PCF.1 6 PLIP interactions: 3 interactions with chain E, 2 interactions with chain D, 1 interactions with chain C Hydrophobic interactions: E:A.41 Hydrogen bonds: E:S.43, E:S.50, D:T.212, C:N.74 Salt bridges: D:K.211

2 x PEF: DI-PALMITOYL-3-SN-PHOSPHATIDYLETHANOLAMINE(Non-covalent)

PEF.8: 17 residues within 4Å: Chain C: W.29, F.94, M.95, M.97, A.98, Y.102, Y.103, F.326, F.327, F.329, V.330, F.333 Chain G: E.80 Chain H: R.50, F.51, Q.54, V.58 12 PLIP interactions: 9 interactions with chain C, 2 interactions with chain H, 1 interactions with chain G Hydrophobic interactions: C:W.29, C:F.94, C:A.98, C:F.326, C:F.329, C:V.330, C:F.333, H:F.51, H:V.58 Hydrogen bonds: C:Y.102, C:Y.103, G:E.80 PEF.10: 4 residues within 4Å: Chain C: F.3, N.7, Y.9, V.13 3 PLIP interactions: 3 interactions with chain C Hydrophobic interactions: C:V.13 Hydrogen bonds: C:N.7 Water bridges: C:V.8

1 x CDL: CARDIOLIPIN(Non-covalent)

CDL.9: 18 residues within 4Å: Chain C: N.27, Y.28, W.29, M.32, L.35, F.88, M.95, V.231, T.232, L.235, F.236, L.238, I.239 Chain D: Y.220, I.224, K.227, K.228 Chain G: H.83 15 PLIP interactions: 8 interactions with chain C, 6 interactions with chain D, 1 interactions with chain G Hydrophobic interactions: C:L.35, C:F.88, C:F.88, C:L.235, C:L.238, C:I.239 Hydrogen bonds: C:Y.28, C:Y.28, D:Y.220 Water bridges: D:K.227, D:K.227, D:K.227 Salt bridges: D:K.227, D:K.228, G:H.83

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

FES.12: 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

Lange, C. et al., SPECIFIC ROLES OF PROTEIN-PHOSPHOLIPID INTERACTIONS IN THE YEAST CYTOCHROME BC1 COMPLEX STRUCTURE. EMBO J. (2001)

Release Date

2002-09-18

Peptides

UBIQUINOL-CYTOCHROME C REDUCTASE COMPLEX CORE PROTEIN I: A
UBIQUINOL-CYTOCHROME C REDUCTASE COMPLEX CORE PROTEIN 2: B
CYTOCHROME B: C
CYTOCHROME C1, HEME PROTEIN: D
UBIQUINOL-CYTOCHROME C REDUCTASE IRON-SULFUR SUBUNIT: E
UBIQUINOL-CYTOCHROME C REDUCTASE COMPLEX 17 KD PROTEIN: F
UBIQUINOL-CYTOCHROME C REDUCTASE COMPLEX 14 KD PROTEIN: G
UBIQUINOL-CYTOCHROME C REDUCTASE COMPLEX UBIQUINONE-BINDING PROTEIN QP-C: H
UBIQUINOL-CYTOCHROME C REDUCTASE COMPLEX 7.3 KD PROTEIN: I
HEAVY CHAIN (VH) OF FV-FRAGMENT: J
LIGHT CHAIN (VL) OF FV-FRAGMENT: K

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

G
G

H
H

I
I

J
J

K
K

Membrane

We predict this structure to be a membrane protein.
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UBIQUINOL-CYTOCHROME C REDUCTASE COMPLEX CORE PROTEIN I

UBIQUINOL-CYTOCHROME C REDUCTASE COMPLEX CORE PROTEIN 2

CYTOCHROME B

CYTOCHROME C1, HEME PROTEIN

UBIQUINOL-CYTOCHROME C REDUCTASE IRON-SULFUR SUBUNIT

UBIQUINOL-CYTOCHROME C REDUCTASE COMPLEX 17 KD PROTEIN

UBIQUINOL-CYTOCHROME C REDUCTASE COMPLEX 14 KD PROTEIN

UBIQUINOL-CYTOCHROME C REDUCTASE COMPLEX UBIQUINONE-BINDING PROTEIN QP-C

UBIQUINOL-CYTOCHROME C REDUCTASE COMPLEX 7.3 KD PROTEIN

HEAVY CHAIN (VH) OF FV-FRAGMENT

LIGHT CHAIN (VL) OF FV-FRAGMENT

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