SMTL ID : 1kyo.1

YEAST CYTOCHROME BC1 COMPLEX WITH BOUND SUBSTRATE CYTOCHROME C

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.97 Å

Oligo State

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

Ligands

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

HEC.1: 21 residues within 4Å: Chain C: Q.43, I.44, G.47, I.48, M.50, A.51, Y.54, V.65, R.79, H.82, A.83, A.86, T.127, A.128, G.131, Y.132, V.135, F.180, H.183, Y.184, P.187 17 PLIP interactions: 17 interactions with chain C, Hydrophobic interactions: C:Q.43, C:I.44, C:A.51, C:Y.54, C:V.65, C:A.86, C:T.127, C:F.180, C:Y.184 Salt bridges: C:R.79, C:R.79 pi-Stacking: C:H.82, C:H.82, C:H.183, C:H.183 Metal complexes: C:H.82, C:H.183 HEC.2: 22 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 24 PLIP interactions: 24 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:G.33, C:S.105, C:S.206, C:S.206, C:S.207 Salt bridges: C:H.96, C:K.99, C:K.99 Metal complexes: C:H.96, C:H.197 HEC.4: 18 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.133, L.134, F.157, I.162, A.163, M.164, V.167 16 PLIP interactions: 16 interactions with chain D, Hydrophobic interactions: D:P.114, D:I.119, D:I.130, D:L.133, D:L.134, D:I.162, D:A.163, D:M.164, D:V.167, D:V.167 Hydrogen bonds: D:Y.129, D:Y.129, D:A.163 Salt bridges: D:R.123 pi-Stacking: D:H.44 Metal complexes: D:H.44 HEC.6: 22 residues within 4Å: Chain N: L.40, Q.43, G.47, I.48, M.50, A.51, Y.54, R.79, H.82, A.83, A.86, F.89, T.127, A.128, G.131, Y.132, V.135, F.180, H.183, Y.184, P.187, Y.274 17 PLIP interactions: 17 interactions with chain N, Hydrophobic interactions: N:L.40, N:Q.43, N:A.51, N:Y.54, N:A.86, N:F.89, N:T.127, N:F.180, N:Y.184 Salt bridges: N:R.79, N:R.79 pi-Stacking: N:H.82, N:H.82, N:H.183 pi-Cation interactions: N:H.82 Metal complexes: N:H.82, N:H.183 HEC.7: 19 residues within 4Å: Chain N: W.29, W.30, G.33, L.36, M.93, H.96, M.97, K.99, S.105, L.113, W.114, G.117, I.120, V.194, H.197, L.198, L.201, S.206, S.207 19 PLIP interactions: 19 interactions with chain N, Hydrophobic interactions: N:L.36, N:L.36, N:L.113, N:W.114, N:I.120, N:L.198, N:L.201 Hydrogen bonds: N:G.33, N:S.105, N:S.206, N:S.206, N:S.207 Salt bridges: N:H.96, N:K.99, N:K.99 pi-Stacking: N:H.96, N:H.197 Metal complexes: N:H.96, N:H.197 HEC.9: 20 residues within 4Å: Chain O: V.39, C.40, C.43, H.44, N.108, A.111, P.113, P.114, L.116, R.123, Y.129, I.130, L.133, L.134, F.157, I.162, A.163, M.164, V.167, L.168 17 PLIP interactions: 17 interactions with chain O, Hydrophobic interactions: O:V.39, O:A.111, O:P.113, O:P.114, O:L.116, O:L.116, O:I.130, O:L.133, O:L.134, O:I.162, O:A.163, O:M.164, O:V.167, O:L.168 Hydrogen bonds: O:A.163 Salt bridges: O:R.123 Metal complexes: O:H.44 HEC.11: 24 residues within 4Å: Chain W: F.15, R.18, C.19, C.22, H.23, V.33, G.34, L.37, I.40, S.45, G.46, Y.51, Y.53, T.54, N.57, W.64, M.69, Y.72, L.73, T.83, K.84, M.85, A.86, F.87 18 PLIP interactions: 18 interactions with chain W, Hydrophobic interactions: W:F.15, W:V.33, W:V.33, W:L.37, W:Y.53, W:Y.72, W:L.73, W:M.85, W:F.87, W:F.87 Hydrogen bonds: W:G.46, W:Y.53, W:T.54, W:N.57, W:N.57, W:T.83, W:K.84 Metal complexes: W:H.23

2 x SMA: STIGMATELLIN A(Non-covalent)

SMA.3: 23 residues within 4Å: Chain C: T.122, I.125, A.126, F.129, L.130, M.139, G.143, V.146, I.147, F.151, L.165, L.182, I.269, V.270, P.271, E.272, L.275, F.278, Y.279, M.295, F.296 Chain P: C.150, H.151 8 PLIP interactions: 8 interactions with chain C Hydrophobic interactions: C:F.129, C:L.130, C:F.151, C:L.165, C:L.182, C:L.275, C:F.278 Hydrogen bonds: C:E.272 SMA.8: 21 residues within 4Å: Chain E: C.150, H.151 Chain N: T.122, I.125, A.126, F.129, L.130, M.139, G.143, V.146, I.147, F.151, L.165, I.269, P.271, E.272, L.275, F.278, Y.279, M.295, F.296 10 PLIP interactions: 10 interactions with chain N Hydrophobic interactions: N:I.125, N:F.129, N:F.129, N:L.130, N:F.151, N:L.165, N:L.275, N:L.275, N:F.278 Hydrogen bonds: N:E.272

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

FES.5: 9 residues within 4Å: Chain E: C.129, H.131, L.132, G.133, C.134, C.148, C.150, H.151, 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.10: 11 residues within 4Å: Chain P: C.129, H.131, L.132, G.133, C.134, C.148, C.150, H.151, G.152, S.153, P.165 4 PLIP interactions: 4 interactions with chain P, Metal complexes: P:C.129, P:H.131, P:C.148, P:H.151

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Lange, C. et al., Crystal structure of the yeast cytochrome bc1 complex with its bound substrate cytochrome c. Proc.Natl.Acad.Sci.USA (2002)

Release Date

2002-03-06

Peptides

UBIQUINOL-CYTOCHROME C REDUCTASE COMPLEX CORE PROTEIN I: AL
UBIQUINOL-CYTOCHROME C REDUCTASE COMPLEX CORE PROTEIN 2: BM
CYTOCHROME B: CN
CYTOCHROME C1, HEME PROTEIN: DO
UBIQUINOL-CYTOCHROME C REDUCTASE IRON-SULFUR SUBUNIT: EP
UBIQUINOL-CYTOCHROME C REDUCTASE COMPLEX 17 KD PROTEIN: FQ
UBIQUINOL-CYTOCHROME C REDUCTASE COMPLEX 14 KD PROTEIN: GR
UBIQUINOL-CYTOCHROME C REDUCTASE COMPLEX UBIQUINONE-BINDING PROTEIN QP-C: HS
UBIQUINOL-CYTOCHROME C REDUCTASE COMPLEX 7.3 KD PROTEIN: IT
HEAVY CHAIN (VH) OF FV-FRAGMENT: JU
LIGHT CHAIN (VL) OF FV-FRAGMENT: KV
CYTOCHROME C, ISO-1: W

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

L
L

B
B

M
M

C
C

N
N

D
D

O
O

E
E

P
P

F
F

Q
Q

G
G

R
R

H
H

S
S

I
I

T
T

J
J

U
U

K
K

V
V

W
W

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

CYTOCHROME C, ISO-1

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