SMTL ID : 1ppj.1

Bovine cytochrome bc1 complex with stigmatellin and antimycin

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

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

Ligands

9 x JZR: hexyl beta-D-glucopyranoside(Non-covalent)

JZR.1: 6 residues within 4Å: Chain A: P.391, A.393, E.394, S.397, R.398, E.401 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:E.394, A:R.398, A:E.401 Hydrogen bonds: A:E.394, A:S.397, A:S.397 Water bridges: A:Q.9, A:Q.9, A:S.397 JZR.5: 3 residues within 4Å: Chain C: L.249, G.251 Chain D: H.121 No protein-ligand interaction detected (PLIP) JZR.6: 6 residues within 4Å: Chain C: H.345, T.349, I.350, L.353 Chain G: V.58, W.61 8 PLIP interactions: 5 interactions with chain C, 3 interactions with chain G Hydrophobic interactions: C:T.349, C:I.350, C:L.353, G:V.58, G:W.61, G:W.61 Hydrogen bonds: C:T.349 Salt bridges: C:H.345 JZR.16: 8 residues within 4Å: Chain D: C.135, E.136, P.137, E.145, G.146, L.147, Y.148, F.149 3 PLIP interactions: 3 interactions with chain D Hydrophobic interactions: D:P.137 Hydrogen bonds: D:E.145, D:G.146 JZR.21: 9 residues within 4Å: Chain F: R.49, E.100, R.104 Chain K: H.289 Chain L: T.76, S.81, S.82, F.83, E.136 10 PLIP interactions: 4 interactions with chain L, 1 interactions with chain K, 5 interactions with chain F Hydrogen bonds: L:T.76, L:S.81, L:S.82, L:F.83, F:R.104 Salt bridges: K:H.289, F:R.104 Water bridges: F:R.49, F:E.100, F:E.100 JZR.22: 1 residues within 4Å: Chain F: W.19 No protein-ligand interaction detected (PLIP) JZR.28: 6 residues within 4Å: Chain M: L.249, L.250, G.251, K.269, W.272 Chain N: H.121 3 PLIP interactions: 3 interactions with chain M Hydrophobic interactions: M:L.249 Hydrogen bonds: M:L.249, M:K.269 JZR.40: 3 residues within 4Å: Chain M: Y.75 Chain O: S.56, S.60 1 PLIP interactions: 1 interactions with chain M Hydrogen bonds: M:Y.75 JZR.43: 11 residues within 4Å: Chain A: H.289 Chain B: L.75, S.82, F.83, E.136, A.139, L.140 Chain P: E.45, R.49, E.100, R.104 12 PLIP interactions: 5 interactions with chain B, 6 interactions with chain P, 1 interactions with chain A Hydrophobic interactions: B:L.75, B:E.136, B:E.136, B:A.139, B:L.140 Hydrogen bonds: P:E.45, P:R.49, P:R.104, P:R.104 Water bridges: P:R.48, P:E.100 Salt bridges: A:H.289

5 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.2: 2 residues within 4Å: Chain A: S.439 Chain C: H.221 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain C Hydrogen bonds: A:S.439, A:S.439 Salt bridges: C:H.221 PO4.8: 2 residues within 4Å: Chain C: Y.75 Chain E: S.56 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:S.56 PO4.23: 2 residues within 4Å: Chain F: Y.93 Chain L: R.134 2 PLIP interactions: 1 interactions with chain L, 1 interactions with chain F Salt bridges: L:R.134 Water bridges: F:Y.93 PO4.30: 2 residues within 4Å: Chain K: S.439 Chain M: H.221 2 PLIP interactions: 1 interactions with chain M, 1 interactions with chain K Salt bridges: M:H.221 Hydrogen bonds: K:S.439 PO4.44: 2 residues within 4Å: Chain B: R.134 Chain P: Y.93 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain P Salt bridges: B:R.134 Hydrogen bonds: P:Y.93

5 x AZI: AZIDE ION(Non-covalent)

AZI.3: 8 residues within 4Å: Chain A: L.62, K.65, G.66, C.120, S.121, L.122, E.123, Q.126 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:L.62, A:S.121, A:L.122, A:E.123 AZI.7: 4 residues within 4Å: Chain C: V.66, R.80, N.255, Y.256 4 PLIP interactions: 3 interactions with chain C, 1 interactions with chain D Hydrogen bonds: C:R.80, C:R.80, D:Y.115 Water bridges: C:N.255 AZI.24: 7 residues within 4Å: Chain D: H.225, S.228 Chain E: R.15 Chain G: P.20, Q.23, R.24, A.25 3 PLIP interactions: 1 interactions with chain G, 1 interactions with chain D, 1 interactions with chain E Hydrogen bonds: G:P.20, D:S.228, E:R.15 AZI.26: 5 residues within 4Å: Chain L: T.101, D.380, S.384 Chain S: V.65 Ligands: GOL.27 2 PLIP interactions: 2 interactions with chain L Hydrogen bonds: L:S.384, L:S.384 AZI.29: 5 residues within 4Å: Chain M: V.66, R.80, N.255, Y.256 Chain N: Y.115 4 PLIP interactions: 4 interactions with chain M Hydrogen bonds: M:R.80, M:R.80, M:N.255 Water bridges: M:T.67

6 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 6 residues within 4Å: Chain B: T.101, E.103, N.104, S.315, Y.316 Chain I: P.63 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:T.101, B:E.103, B:N.104 GOL.14: 8 residues within 4Å: Chain C: A.84, A.87, Y.131, L.250, G.251, E.271, Y.273 Ligands: HEM.9 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:L.250, C:Y.273 GOL.15: 1 residues within 4Å: Chain C: T.158 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:T.158, C:T.158 GOL.27: 7 residues within 4Å: Chain L: T.101, E.103, N.104, S.315, Y.316 Chain S: P.63 Ligands: AZI.26 2 PLIP interactions: 2 interactions with chain L Hydrogen bonds: L:E.103, L:N.104 GOL.37: 9 residues within 4Å: Chain M: A.84, A.87, S.88, Y.131, L.250, G.251, E.271, Y.273 Ligands: HEM.31 3 PLIP interactions: 3 interactions with chain M Hydrogen bonds: M:S.88, M:L.250 Water bridges: M:D.252 GOL.42: 4 residues within 4Å: Chain C: F.168 Chain O: M.71, R.92, K.94 2 PLIP interactions: 2 interactions with chain O Hydrogen bonds: O:R.92, O:K.94

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

HEM.9: 23 residues within 4Å: Chain C: L.41, Q.44, I.45, G.48, L.49, L.51, A.52, Y.55, R.80, H.83, A.87, F.90, T.126, A.127, G.130, Y.131, L.133, P.134, H.182, F.183, P.186, Y.273 Ligands: GOL.14 19 PLIP interactions: 19 interactions with chain C, Hydrophobic interactions: C:L.41, C:Q.44, C:I.45, C:L.49, C:L.51, C:Y.55, C:A.87, C:F.90, C:T.126, C:L.133, C:L.133, C:F.183 Water bridges: C:R.80, C:R.80 Salt bridges: C:R.80, C:R.80 pi-Stacking: C:H.182 Metal complexes: C:H.83, C:H.182 HEM.10: 21 residues within 4Å: Chain C: W.31, G.34, L.37, G.38, H.97, V.98, R.100, S.106, F.109, T.112, W.113, G.116, V.117, L.119, L.120, H.196, L.197, L.200, S.205, N.206 Ligands: ANY.13 23 PLIP interactions: 23 interactions with chain C, Hydrophobic interactions: C:L.37, C:L.37, C:T.112, C:W.113, C:W.113, C:V.117, C:L.119, C:L.119, C:L.120, C:L.197, C:L.200, C:L.200 Hydrogen bonds: C:G.34, C:S.106, C:N.206, C:N.206 Water bridges: C:W.31, C:S.35 Salt bridges: C:H.97, C:R.100, C:R.100 Metal complexes: C:H.97, C:H.196 HEM.31: 23 residues within 4Å: Chain M: L.41, Q.44, I.45, G.48, L.49, L.51, A.52, Y.55, R.80, H.83, A.87, F.90, T.126, A.127, G.130, Y.131, L.133, P.134, H.182, F.183, P.186, Y.273 Ligands: GOL.37 20 PLIP interactions: 20 interactions with chain M, Hydrophobic interactions: M:L.41, M:Q.44, M:I.45, M:L.49, M:L.51, M:Y.55, M:A.87, M:F.90, M:T.126, M:L.133, M:L.133, M:F.183 Water bridges: M:R.80, M:R.80 Salt bridges: M:R.80, M:R.80 pi-Stacking: M:H.83, M:H.182 Metal complexes: M:H.83, M:H.182 HEM.32: 20 residues within 4Å: Chain M: W.31, G.34, L.37, H.97, V.98, R.100, S.106, F.109, T.112, W.113, G.116, V.117, L.119, L.120, H.196, L.197, L.200, S.205, N.206 Ligands: ANY.36 24 PLIP interactions: 24 interactions with chain M, Hydrophobic interactions: M:L.37, M:L.37, M:T.112, M:W.113, M:W.113, M:V.117, M:L.119, M:L.120, M:L.197, M:L.200, M:L.200 Hydrogen bonds: M:W.31, M:G.34, M:S.106, M:S.106, M:N.206, M:N.206 Water bridges: M:F.33, M:S.35 Salt bridges: M:H.97, M:R.100, M:R.100 Metal complexes: M:H.97, M:H.196

2 x SMA: STIGMATELLIN A(Non-covalent)

SMA.11: 18 residues within 4Å: Chain C: L.121, M.124, A.125, F.128, M.129, M.138, G.142, V.145, I.146, K.269, P.270, E.271, F.274, A.277, Y.278, I.298 Chain O: C.160, H.161 8 PLIP interactions: 8 interactions with chain C Hydrophobic interactions: C:F.128, C:F.128, C:I.146, C:P.270, C:F.274, C:F.274, C:A.277 Hydrogen bonds: C:E.271 SMA.33: 19 residues within 4Å: Chain E: C.160, H.161 Chain M: L.121, M.124, A.125, F.128, M.129, M.138, G.142, V.145, I.146, I.164, K.269, P.270, E.271, F.274, A.277, Y.278, L.294 9 PLIP interactions: 9 interactions with chain M Hydrophobic interactions: M:F.128, M:F.128, M:I.146, M:I.164, M:F.274, M:F.274, M:F.274, M:A.277 Hydrogen bonds: M:E.271

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

PEE.12: 20 residues within 4Å: Chain C: W.30, Y.95, M.96, G.99, R.100, L.102, Y.103, Y.104, F.276, M.316, Q.322, F.325, W.326, V.329, L.332, T.336 Chain F: Q.72 Chain G: C.44, V.48 Ligands: CDL.25 15 PLIP interactions: 14 interactions with chain C, 1 interactions with chain F Hydrophobic interactions: C:W.30, C:W.30, C:L.102, C:Y.103, C:Y.103, C:F.276, C:F.276, C:F.325, C:W.326, C:L.332, C:L.332 Hydrogen bonds: C:Y.103, C:Y.104, F:Q.72 Water bridges: C:Q.322 PEE.19: 16 residues within 4Å: Chain C: I.78, M.82, M.240 Chain D: H.200, R.203, M.204, K.207, M.208, M.211 Chain E: Y.49, A.50, N.53, V.54, Q.57 Chain J: D.36, D.40 7 PLIP interactions: 4 interactions with chain E, 3 interactions with chain D Hydrophobic interactions: E:A.50, E:V.54, D:M.211 Hydrogen bonds: E:Y.49, E:Q.57, D:R.203 Salt bridges: D:K.207 PEE.35: 20 residues within 4Å: Chain M: W.30, Y.95, M.96, G.99, R.100, L.102, Y.103, Y.104, F.276, M.316, Q.322, F.325, W.326, V.329, L.332, T.336 Chain P: Q.72 Chain Q: C.44, V.48 Ligands: CDL.45 14 PLIP interactions: 13 interactions with chain M, 1 interactions with chain P Hydrophobic interactions: M:W.30, M:W.30, M:L.102, M:Y.103, M:F.276, M:F.276, M:F.325, M:W.326, M:L.332, M:L.332 Hydrogen bonds: M:Y.103, M:Y.104, P:Q.72 Water bridges: M:Q.322 PEE.39: 18 residues within 4Å: Chain M: L.43, M.82, L.233, I.236, M.240 Chain N: H.200, R.203, M.204, K.207, M.208, M.211, M.212 Chain O: Y.49, A.50, A.51, N.53, V.54, Q.57 7 PLIP interactions: 4 interactions with chain O, 2 interactions with chain N, 1 interactions with chain M Hydrophobic interactions: O:A.50, O:A.51, M:I.236 Hydrogen bonds: O:N.53 Water bridges: O:N.53 Salt bridges: N:H.200, N:K.207

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.13: 15 residues within 4Å: Chain C: A.17, I.27, W.31, N.32, G.34, S.35, G.38, L.41, M.194, L.197, S.205, F.220, Y.224, D.228 Ligands: HEM.10 7 PLIP interactions: 7 interactions with chain C Hydrophobic interactions: C:I.27, C:L.41, C:L.197, C:F.220 Hydrogen bonds: C:D.228, C:D.228 pi-Stacking: C:F.220 ANY.36: 16 residues within 4Å: Chain M: A.17, I.27, W.31, N.32, G.34, S.35, G.38, L.41, M.190, M.194, L.197, S.205, F.220, Y.224, D.228 Ligands: HEM.32 7 PLIP interactions: 7 interactions with chain M Hydrophobic interactions: M:I.27, M:L.41, M:L.197, M:F.220 Hydrogen bonds: M:D.228, M:D.228 pi-Stacking: M:F.220

2 x HEC: HEME C(Covalent)

HEC.17: 20 residues within 4Å: Chain D: V.36, C.37, S.39, C.40, H.41, N.105, A.108, L.109, P.110, P.111, I.116, R.120, Y.126, L.130, F.153, I.158, G.159, M.160, P.163, I.164 17 PLIP interactions: 17 interactions with chain D, Hydrophobic interactions: D:N.105, D:A.108, D:P.110, D:P.111, D:I.116, D:L.130, D:F.153, D:I.158, D:M.160, D:P.163, D:I.164 Hydrogen bonds: D:Y.126, D:G.159 Water bridges: D:L.109 Salt bridges: D:R.120 pi-Stacking: D:H.41 Metal complexes: D:H.41 HEC.38: 20 residues within 4Å: Chain N: V.36, C.37, S.39, C.40, H.41, N.105, A.108, L.109, P.110, P.111, I.116, R.120, Y.126, L.130, F.153, I.158, G.159, M.160, P.163, I.164 17 PLIP interactions: 17 interactions with chain N, Hydrophobic interactions: N:N.105, N:A.108, N:P.110, N:P.111, N:I.116, N:F.153, N:I.158, N:M.160, N:P.163, N:I.164 Hydrogen bonds: N:Y.126, N:Y.126, N:G.159 Salt bridges: N:R.120 pi-Stacking: N:H.41, N:H.41 Metal complexes: N:H.41

4 x CDL: CARDIOLIPIN(Non-covalent)

CDL.18: 17 residues within 4Å: Chain C: S.29, N.32, L.36, M.89, K.227, L.230, G.231, L.234, L.235 Chain D: Y.220, K.223, R.224, K.231 Chain F: M.70 Chain G: G.33, N.36, R.40 16 PLIP interactions: 5 interactions with chain C, 3 interactions with chain G, 7 interactions with chain D, 1 interactions with chain F Hydrophobic interactions: C:N.32, C:L.36, C:L.230, C:L.234, D:Y.220 Salt bridges: C:K.227, G:R.40, D:K.223, D:R.224, D:K.231 Hydrogen bonds: G:N.36, D:K.231, F:M.70 Water bridges: G:R.40, D:K.223, D:K.231 CDL.25: 11 residues within 4Å: Chain C: S.28, S.29, W.30, F.33, I.92, M.96 Chain F: Q.72 Chain G: R.40, T.41, C.44 Ligands: PEE.12 10 PLIP interactions: 1 interactions with chain F, 5 interactions with chain G, 4 interactions with chain C Hydrogen bonds: F:Q.72, C:S.29, C:W.30 Water bridges: G:R.40, G:R.40 Salt bridges: G:R.40, G:R.40, G:R.40 Hydrophobic interactions: C:W.30, C:I.92 CDL.34: 18 residues within 4Å: Chain M: S.29, N.32, L.36, M.89, K.227, L.230, G.231, L.234 Chain N: Y.220, K.223, R.224, K.231 Chain P: M.70, R.71, Q.72 Chain Q: N.36, R.40 Ligands: CDL.45 18 PLIP interactions: 6 interactions with chain M, 7 interactions with chain N, 1 interactions with chain P, 4 interactions with chain Q Hydrophobic interactions: M:N.32, M:L.36, M:L.234 Hydrogen bonds: M:S.29, M:N.32, N:K.231, P:M.70, Q:N.36 Salt bridges: M:K.227, N:K.223, N:R.224, N:K.231, Q:R.40 Water bridges: N:K.223, N:R.224, N:K.231, Q:R.40, Q:R.40 CDL.45: 12 residues within 4Å: Chain M: S.28, S.29, W.30, F.33, I.92, M.96 Chain P: Q.72 Chain Q: V.37, R.40, T.41 Ligands: CDL.34, PEE.35 11 PLIP interactions: 4 interactions with chain M, 2 interactions with chain P, 5 interactions with chain Q Hydrophobic interactions: M:W.30, M:I.92, M:I.92 Hydrogen bonds: M:S.29, P:Q.72, P:Q.72 Water bridges: Q:R.40, Q:R.40 Salt bridges: Q:R.40, Q:R.40, Q:R.40

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

FES.20: 10 residues within 4Å: Chain E: 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 E, Metal complexes: E:C.139, E:H.141, E:C.158, E:H.161 FES.41: 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

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Huang, L.S. et al., Binding of the Respiratory Chain Inhibitor Antimycin to the Mitochondrial bc(1) Complex: A New Crystal Structure Reveals an Altered Intramolecular Hydrogen-bonding Pattern. J.Mol.Biol. (2005)

Release Date

2004-07-20

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
Ubiquinol-cytochrome C reductase iron-sulfur subunit, 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
Ubiquinol-cytochrome C reductase iron-sulfur subunit, 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.
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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

Ubiquinol-cytochrome C reductase iron-sulfur subunit, 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

Ubiquinol-cytochrome C reductase iron-sulfur subunit, mitochondrial

Ubiquinol-cytochrome C reductase complex 7.2 kDa protein

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