SMTL ID : 3h1i.1

Stigmatellin and antimycin bound cytochrome bc1 complex from chicken

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 3.53 Å

Oligo State

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

Ligands

6 x PEE: 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine(Non-covalent)

PEE.1: 5 residues within 4Å: Chain A: S.439, Y.442 Chain C: H.222, I.230 Ligands: PEE.16 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain C Hydrogen bonds: A:S.439 Hydrophobic interactions: C:I.230 Salt bridges: C:H.222 PEE.8: 16 residues within 4Å: Chain C: W.31, F.96, I.99, G.100, R.101, Y.104, Y.105, F.277, T.317, F.326, W.327, L.333 Chain F: Y.29 Chain G: Q.44, V.48 Ligands: CDL.7 16 PLIP interactions: 16 interactions with chain C Hydrophobic interactions: C:W.31, C:W.31, C:W.31, C:F.96, C:I.99, C:Y.104, C:Y.105, C:F.277, C:F.277, C:F.326, C:W.327, C:W.327, C:L.333 Hydrogen bonds: C:Y.104, C:Y.104, C:Y.105 PEE.16: 12 residues within 4Å: Chain A: Y.442 Chain C: F.227, I.230 Chain D: K.226 Chain E: Y.37, T.40, T.47 Chain J: F.11, F.17, V.26, E.29 Ligands: PEE.1 6 PLIP interactions: 2 interactions with chain E, 1 interactions with chain J, 1 interactions with chain C, 1 interactions with chain D, 1 interactions with chain A Hydrophobic interactions: E:T.47, J:V.26, C:I.230 Hydrogen bonds: E:Y.37, A:Y.442 Salt bridges: D:K.226 PEE.20: 4 residues within 4Å: Chain K: S.439, Y.442 Chain M: H.222 Ligands: PEE.27 4 PLIP interactions: 1 interactions with chain M, 3 interactions with chain K Salt bridges: M:H.222 Hydrogen bonds: K:S.439, K:Y.442, K:Y.442 PEE.27: 16 residues within 4Å: Chain K: Y.442 Chain M: F.227, I.230, L.233 Chain N: K.226 Chain O: Y.37, T.40, T.47, A.48, K.52 Chain T: F.11, T.14, F.17, V.26, E.29 Ligands: PEE.20 5 PLIP interactions: 1 interactions with chain N, 1 interactions with chain M, 3 interactions with chain O Salt bridges: N:K.226 Hydrophobic interactions: M:L.233, O:A.48 Hydrogen bonds: O:Y.37, O:T.40 PEE.28: 16 residues within 4Å: Chain M: W.31, F.96, G.100, R.101, Y.104, Y.105, F.277, T.317, F.326, W.327, L.333, T.337 Chain P: Y.29 Chain Q: Q.44, V.48 Ligands: CDL.26 14 PLIP interactions: 13 interactions with chain M, 1 interactions with chain Q Hydrophobic interactions: M:W.31, M:W.31, M:F.96, M:Y.104, M:Y.105, M:F.277, M:F.277, M:F.326, M:F.326, M:W.327, M:W.327, M:L.333 Hydrogen bonds: M:Y.104, Q:Q.44

10 x UNL: UNKNOWN LIGAND(Non-covalent)(Non-functional Binders)

UNL.2: 1 residues within 4Å: Chain B: S.84 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:S.84, B:S.84 UNL.9: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) UNL.11: 1 residues within 4Å: Chain C: N.149 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:N.149 UNL.12: 2 residues within 4Å: Chain C: T.199, H.202 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:T.199, C:H.202 UNL.18: 1 residues within 4Å: Chain E: Y.178 No protein-ligand interaction detected (PLIP) UNL.19: 2 residues within 4Å: Chain E: T.140 Chain M: N.149 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:T.140 UNL.23: 1 residues within 4Å: Chain M: T.199 1 PLIP interactions: 1 interactions with chain M Hydrogen bonds: M:H.202 UNL.29: 2 residues within 4Å: Chain M: A.85 Ligands: HEM.21 1 PLIP interactions: 1 interactions with chain M Hydrogen bonds: M:A.85 UNL.31: 3 residues within 4Å: Chain M: N.149, H.159, W.166 2 PLIP interactions: 2 interactions with chain M Hydrogen bonds: M:N.149, M:H.159 UNL.35: 3 residues within 4Å: Chain C: N.149 Chain O: T.140, H.141 1 PLIP interactions: 1 interactions with chain O Hydrogen bonds: O:H.141

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

HEM.3: 21 residues within 4Å: Chain C: Q.45, I.46, G.49, L.50, L.52, A.53, Y.56, R.81, H.84, A.85, L.124, T.127, A.128, G.131, Y.132, L.134, P.135, F.180, H.183, F.184, P.187 20 PLIP interactions: 20 interactions with chain C, Hydrophobic interactions: C:Q.45, C:I.46, C:L.52, C:L.52, C:A.53, C:Y.56, C:L.124, C:T.127, C:A.128, C:L.134, C:F.180, C:F.184, C:P.187 Salt bridges: C:R.81, C:R.81 pi-Stacking: C:H.84, C:H.183, C:H.183 Metal complexes: C:H.84, C:H.183 HEM.4: 23 residues within 4Å: Chain C: W.32, G.35, S.36, L.38, A.39, H.98, R.101, S.107, Y.110, T.113, W.114, G.117, V.118, L.120, L.121, I.190, T.194, H.197, L.198, L.201, S.206, N.207 Ligands: ANY.6 22 PLIP interactions: 22 interactions with chain C, Hydrophobic interactions: C:L.38, C:L.38, C:Y.110, C:T.113, C:W.114, C:V.118, C:L.120, C:L.120, C:L.121, C:I.190, C:L.198, C:L.201, C:L.201 Hydrogen bonds: C:G.35, C:N.207 Salt bridges: C:H.98, C:R.101, C:R.101 pi-Stacking: C:H.98, C:H.197 Metal complexes: C:H.98, C:H.197 HEM.21: 21 residues within 4Å: Chain M: Q.45, I.46, G.49, L.50, L.52, A.53, Y.56, R.81, H.84, A.85, L.124, T.127, A.128, G.131, Y.132, L.134, P.135, H.183, F.184, P.187 Ligands: UNL.29 17 PLIP interactions: 17 interactions with chain M, Hydrophobic interactions: M:Q.45, M:I.46, M:L.52, M:L.52, M:Y.56, M:Y.56, M:L.124, M:T.127, M:A.128, M:L.134, M:F.184 Salt bridges: M:R.81, M:R.81 pi-Stacking: M:H.84, M:H.183 Metal complexes: M:H.84, M:H.183 HEM.22: 24 residues within 4Å: Chain M: W.32, G.35, S.36, L.38, A.39, I.95, H.98, R.101, S.107, Y.110, T.113, W.114, G.117, V.118, L.120, L.121, I.190, T.194, H.197, L.198, L.201, S.206, N.207 Ligands: ANY.25 22 PLIP interactions: 22 interactions with chain M, Hydrophobic interactions: M:L.38, M:L.38, M:I.95, M:Y.110, M:T.113, M:W.114, M:V.118, M:L.120, M:L.120, M:L.121, M:I.190, M:L.198, M:L.201, M:L.201 Hydrogen bonds: M:G.35, M:N.207 Salt bridges: M:H.98, M:R.101, M:R.101 pi-Stacking: M:H.98 Metal complexes: M:H.98, M:H.197

2 x SMA: STIGMATELLIN A(Non-covalent)

SMA.5: 21 residues within 4Å: Chain C: L.122, M.125, A.126, F.129, G.143, V.146, I.147, T.148, F.151, F.179, L.182, I.269, K.270, P.271, E.272, F.275, A.278, Y.279, L.295 Chain O: C.160, H.161 13 PLIP interactions: 13 interactions with chain C Hydrophobic interactions: C:F.129, C:F.129, C:T.148, C:F.151, C:F.179, C:L.182, C:P.271, C:F.275, C:F.275, C:F.275, C:A.278, C:L.295 Hydrogen bonds: C:E.272 SMA.24: 22 residues within 4Å: Chain E: C.160, H.161 Chain M: L.122, M.125, A.126, F.129, V.130, G.143, V.146, I.147, T.148, F.151, F.179, L.182, I.269, K.270, P.271, E.272, F.275, A.278, Y.279, L.295 14 PLIP interactions: 14 interactions with chain M Hydrophobic interactions: M:F.129, M:F.129, M:V.130, M:T.148, M:F.151, M:F.179, M:L.182, M:F.275, M:F.275, M:F.275, M:A.278, M:L.295 Hydrogen bonds: M:E.272, M:E.272

2 x ANY: 2-METHYL-BUTYRIC ACID 3-(3-FORMYLAMINO-2-HYDROXY-BENZOYLAMINO)-8-HEPTYL-2,6-DIMETHYL-4,9-DIOXO-[1,5]DIOXONAN-7-YL ESTER(Non-covalent)

ANY.6: 17 residues within 4Å: Chain C: S.18, L.19, I.28, W.32, N.33, G.35, S.36, A.39, L.42, T.194, I.195, L.198, S.206, F.221, Y.225, D.229 Ligands: HEM.4 11 PLIP interactions: 11 interactions with chain C Hydrophobic interactions: C:L.19, C:L.19, C:I.28, C:A.39, C:L.42, C:T.194, C:I.195 Hydrogen bonds: C:S.36, C:D.229, C:D.229 pi-Stacking: C:F.221 ANY.25: 18 residues within 4Å: Chain M: S.18, L.19, L.22, I.28, W.32, N.33, G.35, S.36, A.39, L.42, T.194, I.195, L.198, S.206, F.221, Y.225, D.229 Ligands: HEM.22 11 PLIP interactions: 11 interactions with chain M Hydrophobic interactions: M:L.19, M:L.19, M:I.28, M:A.39, M:L.42, M:T.194, M:I.195, M:F.221 Hydrogen bonds: M:S.36, M:D.229, M:D.229

4 x CDL: CARDIOLIPIN(Non-covalent)

CDL.7: 11 residues within 4Å: Chain C: S.29, A.30, W.31, F.34, Y.105 Chain F: H.72 Chain G: R.40, F.41, Q.44 Ligands: PEE.8, CDL.14 8 PLIP interactions: 4 interactions with chain C, 1 interactions with chain F, 3 interactions with chain G Hydrophobic interactions: C:W.31, C:W.31, C:F.34 Hydrogen bonds: C:A.30, G:R.40 Salt bridges: F:H.72, G:R.40, G:R.40 CDL.14: 15 residues within 4Å: Chain C: A.30, N.33, L.231, G.232, L.235, M.236 Chain D: Y.220, K.223, R.224 Chain F: H.72, R.73 Chain G: A.33, L.34, R.40 Ligands: CDL.7 9 PLIP interactions: 4 interactions with chain C, 2 interactions with chain G, 2 interactions with chain D, 1 interactions with chain F Hydrophobic interactions: C:L.235, C:M.236 Hydrogen bonds: C:N.33, G:R.40 Salt bridges: C:K.228, G:R.40, D:K.223, D:R.224, F:R.73 CDL.26: 11 residues within 4Å: Chain M: S.29, A.30, W.31, Y.105 Chain P: H.72 Chain Q: V.37, R.40, F.41, Q.44 Ligands: PEE.28, CDL.33 9 PLIP interactions: 4 interactions with chain M, 1 interactions with chain P, 4 interactions with chain Q Hydrophobic interactions: M:W.31, M:W.31, Q:V.37 Hydrogen bonds: M:A.30, M:Y.105, Q:R.40 Salt bridges: P:H.72, Q:R.40, Q:R.40 CDL.33: 17 residues within 4Å: Chain M: A.30, N.33, L.231, G.232, L.235, M.236 Chain N: Y.220, K.223, R.224, K.231 Chain P: H.72, R.73 Chain Q: I.29, A.33, L.34, R.40 Ligands: CDL.26 12 PLIP interactions: 5 interactions with chain M, 4 interactions with chain N, 2 interactions with chain Q, 1 interactions with chain P Hydrophobic interactions: M:A.30, M:L.235, M:M.236, N:Y.220 Hydrogen bonds: M:N.33, N:Y.220, Q:R.40 Salt bridges: M:K.228, N:K.223, N:R.224, Q:R.40, P:R.73

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.10: 6 residues within 4Å: Chain C: F.64, A.68, R.81, N.256, F.257 Chain D: Y.115 5 PLIP interactions: 1 interactions with chain D, 4 interactions with chain C Hydrogen bonds: D:Y.115, C:R.81, C:R.81, C:N.256, C:N.256 GOL.30: 4 residues within 4Å: Chain M: F.64, R.81, N.256 Chain N: Y.115 4 PLIP interactions: 3 interactions with chain M, 1 interactions with chain N Hydrogen bonds: M:R.81, M:R.81, M:N.256, N:Y.115

2 x HEC: HEME C(Covalent)

HEC.13: 19 residues within 4Å: Chain D: V.32, V.36, C.37, C.40, H.41, N.105, A.108, P.110, P.111, L.113, R.120, Y.126, L.131, F.153, I.158, G.159, M.160, P.163, V.186 13 PLIP interactions: 13 interactions with chain D, Hydrophobic interactions: D:V.32, D:A.108, D:P.110, D:L.113, D:L.131, D:L.131, D:I.158, D:M.160, D:P.163 Hydrogen bonds: D:G.159 Salt bridges: D:R.120 pi-Stacking: D:H.41 Metal complexes: D:H.41 HEC.32: 20 residues within 4Å: Chain N: V.32, V.36, C.37, C.40, H.41, N.105, A.108, P.110, P.111, L.113, R.120, Y.126, V.127, L.131, F.153, I.158, G.159, M.160, P.163, V.186 14 PLIP interactions: 14 interactions with chain N, Hydrophobic interactions: N:V.32, N:A.108, N:P.110, N:V.127, N:L.131, N:I.158, N:M.160, N:P.163 Hydrogen bonds: N:Y.126, N:G.159 Salt bridges: N:R.120 pi-Stacking: N:H.41, N:H.41 Metal complexes: N:H.41

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

FES.15: 8 residues within 4Å: Chain E: C.139, H.141, L.142, C.144, C.158, C.160, H.161, 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.34: 10 residues within 4Å: Chain O: 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 O, Metal complexes: O:C.139, O:H.141, O:C.158, O:H.161

2 x PLC: DIUNDECYL PHOSPHATIDYL CHOLINE(Non-covalent)

PLC.17: 16 residues within 4Å: Chain C: T.44, Y.76, L.79, L.241 Chain D: Q.200, M.204, K.207, M.208, I.211, S.212 Chain E: Y.49, A.50, N.53, V.54, Q.57 Chain J: D.33 9 PLIP interactions: 2 interactions with chain D, 5 interactions with chain E, 2 interactions with chain C Hydrophobic interactions: D:I.211, E:A.50, E:V.54, C:T.44, C:L.241 Salt bridges: D:K.207 Hydrogen bonds: E:Y.49, E:N.53, E:Q.57 PLC.36: 14 residues within 4Å: Chain M: T.44, Y.76, L.79, L.241 Chain N: Q.200, M.204, K.207, M.208 Chain O: Y.49, A.50, N.53, V.54, Q.57 Chain T: D.33 9 PLIP interactions: 5 interactions with chain O, 3 interactions with chain M, 1 interactions with chain N Hydrophobic interactions: O:A.50, O:V.54, M:T.44, M:L.241, M:L.241 Hydrogen bonds: O:N.53, O:N.53, O:Q.57 Salt bridges: N:K.207

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zhang, Z. et al., Electron Transfer by Domain Movement in Cytochrome Bc1. Nature (1998)

Release Date

2009-04-28

Peptides

UBIQUINOL-CYTOCHROME-C REDUCTASE COMPLEX CORE PROTEIN I, MITOCHONDRIAL: AK
UBIQUINOL-CYTOCHROME-C REDUCTASE COMPLEX CORE PROTEIN 2, MITOCHONDRIAL: BL
Cytochrome b: CM
CYTOCHROME C1, HEME PROTEIN, MITOCHONDRIAL: DN
Cytochrome b-c1 complex subunit Rieske, mitochondrial: EO
UBIQUINOL-CYTOCHROME C REDUCTASE COMPLEX 14 KDA PROTEIN: FP
UBIQUINOL-CYTOCHROME C REDUCTASE COMPLEX UBIQUINONE-BINDING PROTEIN QP-C: GQ
UBIQUINOL-CYTOCHROME C REDUCTASE COMPLEX 11 KDA PROTEIN: HR
Cytochrome b-c1 complex subunit Rieske, mitochondrial: IS
UBIQUINOL-CYTOCHROME C REDUCTASE COMPLEX 7.2 KDA PROTEIN: JT

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

K
N

B
B

L
O

C
C

M
P

D
D

N
Q

E
E

O
R

F
F

P
S

G
G

Q
T

H
H

R
U

I
I

S
V

J
J

T
W

Membrane

We predict this structure to be a membrane protein.
Show / Hide

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

Cytochrome b-c1 complex subunit Rieske, mitochondrial

UBIQUINOL-CYTOCHROME C REDUCTASE COMPLEX 14 KDA PROTEIN

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

UBIQUINOL-CYTOCHROME C REDUCTASE COMPLEX 11 KDA PROTEIN

Cytochrome b-c1 complex subunit Rieske, mitochondrial

UBIQUINOL-CYTOCHROME C REDUCTASE COMPLEX 7.2 KDA PROTEIN

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