SMTL ID : 1ezv.1

STRUCTURE OF THE YEAST CYTOCHROME BC1 COMPLEX CO-CRYSTALLIZED WITH AN ANTIBODY FV-FRAGMENT

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

hetero-2-2-2-2-2-2-2-2-2-1-1-mer

Ligands

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

HEM.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 16 PLIP interactions: 16 interactions with chain C, Hydrophobic interactions: C:L.40, C:Q.43, 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.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: UQ6.4 25 PLIP interactions: 25 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:M.32, C:G.33, C:S.105, C:S.207 Water bridges: C:S.34 Salt bridges: C:H.96, C:K.99, C:K.99 Metal complexes: C:H.96, C:H.197 HEM.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 20 PLIP interactions: 20 interactions with chain D, Hydrophobic interactions: D:P.113, 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:V.167, D:L.168, D:L.194 Hydrogen bonds: D:Y.129, 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 HEM.7: 20 residues within 4Å: Chain L: 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 16 PLIP interactions: 16 interactions with chain L, Hydrophobic interactions: L:L.40, L:Q.43, L:Q.43, L:A.51, L:A.83, L:F.89, L:F.89, L:T.127, L:Y.184 Salt bridges: L:R.79, L:R.79 pi-Stacking: L:H.82, L:H.82, L:H.183 Metal complexes: L:H.82, L:H.183 HEM.8: 23 residues within 4Å: Chain L: 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: UQ6.10 25 PLIP interactions: 25 interactions with chain L, Hydrophobic interactions: L:L.36, L:L.36, L:F.89, L:L.113, L:L.113, L:W.114, L:W.114, L:V.118, L:I.120, L:F.121, L:V.194, L:V.194, L:L.198, L:L.201 Hydrogen bonds: L:W.30, L:M.32, L:G.33, L:S.105, L:S.207 Water bridges: L:S.34 Salt bridges: L:H.96, L:K.99, L:K.99 Metal complexes: L:H.96, L:H.197 HEM.11: 19 residues within 4Å: Chain M: 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 19 PLIP interactions: 19 interactions with chain M, Hydrophobic interactions: M:P.113, M:P.113, M:P.114, M:I.119, M:I.130, M:L.134, M:L.134, M:I.162, M:M.164, M:V.167, M:V.167, M:L.168, M:L.194 Hydrogen bonds: M:Y.129, M:A.163 Salt bridges: M:R.123 pi-Stacking: M:H.44 pi-Cation interactions: M:H.44 Metal complexes: M:H.44

2 x SMA: STIGMATELLIN A(Non-covalent)

SMA.3: 21 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 Chain N: C.150, H.151 14 PLIP interactions: 14 interactions with chain C Hydrophobic interactions: C:I.125, C:F.129, C:V.146, C:I.147, C:I.147, C:F.151, C:L.165, C:P.271, C:L.275, C:L.275, C:F.278, C:Y.279 Hydrogen bonds: C:E.272 Water bridges: C:E.272 SMA.9: 21 residues within 4Å: Chain E: C.150, H.151 Chain L: 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 14 PLIP interactions: 14 interactions with chain L Hydrophobic interactions: L:I.125, L:F.129, L:V.146, L:I.147, L:I.147, L:F.151, L:L.165, L:P.271, L:L.275, L:L.275, L:F.278, L:Y.279 Hydrogen bonds: L:E.272 Water bridges: L:E.272

2 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)

UQ6.4: 15 residues within 4Å: Chain C: Y.16, I.17, Q.22, S.34, L.40, I.44, F.49, M.52, V.194, L.198, L.201, S.206, M.221, D.229 Ligands: HEM.2 10 PLIP interactions: 10 interactions with chain C Hydrophobic interactions: C:I.17, C:L.40, C:L.40, C:I.44, C:I.44, C:V.194, C:L.198 Hydrogen bonds: C:Q.22, C:S.206 Water bridges: C:S.20 UQ6.10: 15 residues within 4Å: Chain L: Y.16, I.17, Q.22, S.34, L.40, I.44, F.49, M.52, V.194, L.198, L.201, S.206, M.221, D.229 Ligands: HEM.8 10 PLIP interactions: 10 interactions with chain L Hydrophobic interactions: L:I.17, L:L.40, L:L.40, L:I.44, L:I.44, L:V.194, L:L.198 Hydrogen bonds: L:Q.22, L:S.206 Water bridges: L:S.20

2 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 FES.12: 10 residues within 4Å: Chain N: 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 N, Metal complexes: N:C.129, N:H.131, N:C.148, N:H.151

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Hunte, C. et al., Structure at 2.3 A resolution of the cytochrome bc(1) complex from the yeast Saccharomyces cerevisiae co-crystallized with an antibody Fv fragment. Structure Fold.Des. (2000)

Release Date

2001-05-16

Peptides

UBIQUINOL-CYTOCHROME C REDUCTASE COMPLEX CORE PROTEIN I: AJ
UBIQUINOL-CYTOCHROME C REDUCTASE COMPLEX CORE PROTEIN 2: BK
CYTOCHROME B: CL
CYTOCHROME C1: DM
UBIQUINOL-CYTOCHROME C REDUCTASE IRON-SULFUR SUBUNIT: EN
UBIQUINOL-CYTOCHROME C REDUCTASE COMPLEX 17 KD PROTEIN: FO
UBIQUINOL-CYTOCHROME C REDUCTASE COMPLEX 14 KD PROTEIN: GP
UBIQUINOL-CYTOCHROME C REDUCTASE COMPLEX UBIQUINONE-BINDING PROTEIN QP-C: HQ
UBIQUINOL-CYTOCHROME C REDUCTASE COMPLEX 7.3 KD PROTEIN: IR
HEAVY CHAIN (VH) OF FV-FRAGMENT: S
LIGHT CHAIN (VL) OF FV-FRAGMENT: T

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

J
A

B
B

K
B

C
C

L
C

D
D

M
D

E
E

N
E

F
H

O
H

G
F

P
F

H
G

Q
G

I
I

R
I

S
X

T
Y

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

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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