SMTL ID : 1pp9.1

Bovine cytochrome bc1 complex with stigmatellin bound

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

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

JZR.1: 7 residues within 4Å: Chain A: R.388, P.391, A.393, E.394, S.397, R.398, E.401 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.388, A:E.394, A:S.397, A:S.397 JZR.6: 4 residues within 4Å: Chain C: L.249, G.251, K.269 Chain D: H.121 3 PLIP interactions: 2 interactions with chain C, 1 interactions with chain D Hydrophobic interactions: C:L.249 Hydrogen bonds: C:K.269 Water bridges: D:H.121 JZR.19: 10 residues within 4Å: Chain F: E.45, R.49, E.100, E.103, R.104 Chain K: H.289 Chain L: T.76, S.82, F.83, E.136 14 PLIP interactions: 6 interactions with chain L, 7 interactions with chain F, 1 interactions with chain K Hydrogen bonds: L:T.76, L:S.82, L:S.82, L:F.83, L:E.136, F:R.49, F:E.103, F:R.104 Water bridges: L:T.76, F:R.48 Hydrophobic interactions: F:E.45 Salt bridges: F:R.49, F:R.104, K:H.289 JZR.20: 3 residues within 4Å: Chain F: G.15, I.16, W.19 No protein-ligand interaction detected (PLIP) JZR.27: 4 residues within 4Å: Chain M: L.249, G.251, K.269 Chain N: H.121 2 PLIP interactions: 2 interactions with chain M Hydrophobic interactions: M:L.249 Hydrogen bonds: M:K.269 JZR.39: 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 11 PLIP interactions: 5 interactions with chain P, 5 interactions with chain B, 1 interactions with chain A Hydrogen bonds: P:E.45, P:R.49, P:R.104, P:R.104 Water bridges: P:R.48, B:S.81, B:S.81 Hydrophobic interactions: B:L.75, B:E.136, B:A.139 Salt bridges: A:H.289

4 x AZI: AZIDE ION(Non-covalent)

AZI.2: 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:G.66, A:S.121, A:L.122, A:E.123 AZI.7: 3 residues within 4Å: Chain C: R.80, N.255, Y.256 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:R.80, C:R.80, C:N.255 Water bridges: C:N.255 AZI.15: 7 residues within 4Å: Chain D: H.225, S.228 Chain E: R.15, S.36 Chain G: P.20, Q.23, A.25 3 PLIP interactions: 2 interactions with chain D, 1 interactions with chain E Hydrogen bonds: D:H.225, D:S.228, E:R.15 AZI.28: 4 residues within 4Å: Chain M: V.66, R.80, N.255, Y.256 3 PLIP interactions: 3 interactions with chain M Hydrogen bonds: M:R.80, M:R.80 Water bridges: M:T.67

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

PEE.3: 5 residues within 4Å: Chain A: D.332, D.333, F.336 Chain C: N.15, D.20 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain C Hydrogen bonds: A:D.333, C:N.15 PEE.12: 22 residues within 4Å: Chain C: W.30, Y.95, M.96, V.98, 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, Y.358 Chain F: Q.72 Chain G: C.44, V.48 Ligands: CDL.22 18 PLIP interactions: 17 interactions with chain C, 1 interactions with chain F Hydrophobic interactions: C:W.30, C:W.30, C:W.30, C:W.30, C:Y.95, C:V.98, C:L.102, C:Y.103, C:Y.104, C:F.276, C:F.325, C:F.325, C:W.326, C:W.326 Hydrogen bonds: C:Y.103, C:Y.104, F:Q.72 Water bridges: C:Q.322 PEE.13: 2 residues within 4Å: Chain A: S.439 Chain C: H.221 3 PLIP interactions: 1 interactions with chain C, 2 interactions with chain A Salt bridges: C:H.221 Hydrogen bonds: A:S.439, A:S.439 PEE.17: 19 residues within 4Å: Chain C: L.46, L.233, I.236, M.240 Chain D: H.200, R.203, M.204, K.207, M.208, M.211, M.212, L.215 Chain E: Y.49, A.50, A.51, N.53, V.54, Q.57 Chain J: D.36 8 PLIP interactions: 2 interactions with chain E, 4 interactions with chain D, 2 interactions with chain C Hydrophobic interactions: E:V.54, D:M.211, D:L.215, C:L.46, C:I.236 Hydrogen bonds: E:N.53 Salt bridges: D:H.200, D:K.207 PEE.23: 16 residues within 4Å: Chain D: L.210, G.213, L.214, P.217, L.218, A.221 Chain E: R.15, E.17, F.35, V.39, T.42 Chain G: R.24, A.25, F.26 Chain J: F.31, F.35 10 PLIP interactions: 2 interactions with chain G, 2 interactions with chain J, 4 interactions with chain D, 2 interactions with chain E Hydrogen bonds: G:A.25, G:F.26, E:E.17 Hydrophobic interactions: J:F.31, J:F.35, D:L.210, D:L.214, D:P.217, D:L.218, E:T.42 PEE.24: 3 residues within 4Å: Chain K: S.439, F.442 Chain M: H.221 3 PLIP interactions: 1 interactions with chain M, 1 interactions with chain K, 1 interactions with chain N Salt bridges: M:H.221, N:K.226 Hydrogen bonds: K:S.439 PEE.33: 21 residues within 4Å: Chain M: W.30, Y.95, M.96, V.98, 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.40 15 PLIP interactions: 14 interactions with chain M, 1 interactions with chain P Hydrophobic interactions: M:W.30, M:W.30, M:W.30, M:V.98, M:L.102, M:Y.103, M:Y.104, M:F.276, M:F.276, M:W.326, M:V.329 Hydrogen bonds: M:Y.103, M:Y.104, P:Q.72 Water bridges: M:Q.322 PEE.37: 20 residues within 4Å: Chain M: L.43, L.46, L.233, I.236, M.240 Chain N: H.200, R.203, M.204, K.207, M.208, M.211, M.212, L.215 Chain O: Y.49, A.50, A.51, N.53, V.54, Q.57 Chain T: D.36 9 PLIP interactions: 4 interactions with chain M, 2 interactions with chain O, 3 interactions with chain N Hydrophobic interactions: M:L.43, M:L.43, M:L.46, M:I.236, O:V.54, N:L.215 Hydrogen bonds: O:N.53 Salt bridges: N:H.200, N:K.207 PEE.41: 15 residues within 4Å: Chain N: L.210, G.213, L.214, L.218, A.221 Chain O: P.16, E.17, F.35, L.38, V.39, T.42 Chain Q: R.24, A.25, F.26 Chain T: F.35 10 PLIP interactions: 2 interactions with chain N, 4 interactions with chain O, 3 interactions with chain Q, 1 interactions with chain T Hydrophobic interactions: N:L.214, N:L.218, O:F.35, O:L.38, O:T.42, T:F.35 Hydrogen bonds: O:E.17, Q:A.25, Q:F.26, Q:F.26

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

PO4.4: 2 residues within 4Å: Chain B: R.134 Chain P: Y.93 1 PLIP interactions: 1 interactions with chain B Salt bridges: B:R.134 PO4.25: 2 residues within 4Å: Chain F: Y.93 Chain L: R.134 1 PLIP interactions: 1 interactions with chain L Salt bridges: L:R.134

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 5 residues within 4Å: Chain B: E.103, N.104, I.264, S.315 Chain I: P.63 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:E.103, B:S.384 Water bridges: 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.8 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:L.250 Water bridges: C:D.252 GOL.26: 4 residues within 4Å: Chain L: E.103, I.264, S.315 Chain S: P.63 4 PLIP interactions: 4 interactions with chain L Hydrogen bonds: L:E.103, L:E.103 Water bridges: L:S.384, L:S.384 GOL.34: 8 residues within 4Å: Chain M: A.84, S.88, Y.131, L.250, G.251, E.271, Y.273 Ligands: HEM.29 4 PLIP interactions: 4 interactions with chain M Hydrogen bonds: M:A.84, M:L.250 Water bridges: M:Y.131, M:Y.131

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

HEM.8: 26 residues within 4Å: Chain C: L.41, Q.44, I.45, G.48, L.49, L.51, A.52, Y.55, V.66, R.80, H.83, A.87, F.90, T.126, A.127, G.130, Y.131, L.133, P.134, F.179, H.182, F.183, P.186, I.189, Y.273 Ligands: GOL.14 22 PLIP interactions: 22 interactions with chain C, Hydrophobic interactions: C:L.41, C:Q.44, C:Q.44, C:L.49, C:Y.55, C:V.66, C:A.87, C:F.90, C:T.126, C:L.133, C:L.133, C:F.179, C:F.183, C:I.189 Water bridges: C:R.80 Salt bridges: C:R.80, C:R.80 pi-Stacking: C:H.83, C:H.83, C:H.182 Metal complexes: C:H.83, C:H.182 HEM.9: 23 residues within 4Å: Chain C: W.31, G.34, L.37, F.90, L.94, H.97, V.98, R.100, S.106, F.109, T.112, W.113, G.116, V.117, L.119, L.120, I.189, H.196, L.197, L.200, S.205, N.206 Ligands: UQ.11 26 PLIP interactions: 26 interactions with chain C, Hydrophobic interactions: C:L.37, C:L.37, C:F.90, C:L.94, C:V.98, C:T.112, C:W.113, C:W.113, C:V.117, C:L.119, C:L.120, C:I.189, C:L.197, C:L.200 Hydrogen bonds: C:G.34, C:S.106, C:S.106, C:N.206, C:N.206 Water bridges: C:W.31 Salt bridges: C:H.97, C:R.100, C:R.100 pi-Stacking: C:H.196 Metal complexes: C:H.97, C:H.196 HEM.29: 23 residues within 4Å: Chain M: Q.44, I.45, G.48, L.49, L.51, A.52, Y.55, R.80, H.83, A.84, 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.34 17 PLIP interactions: 17 interactions with chain M, Hydrophobic interactions: 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 Salt bridges: M:R.80, M:R.80 pi-Stacking: M:H.182 Metal complexes: M:H.83, M:H.182 HEM.30: 25 residues within 4Å: Chain M: W.31, G.34, S.35, L.37, F.90, L.94, H.97, V.98, R.100, S.106, F.109, T.112, W.113, G.116, V.117, L.119, L.120, I.189, A.193, H.196, L.197, L.200, S.205, N.206 Ligands: UQ.32 27 PLIP interactions: 27 interactions with chain M, Hydrophobic interactions: M:L.37, M:L.37, M:F.90, M:L.94, M:T.112, M:W.113, M:W.113, M:V.117, M:L.119, M:L.119, M:L.120, M:I.189, M:A.193, M:L.197, M:L.200, M:L.200 Hydrogen bonds: M:G.34, M:S.106, M:N.206, M:N.206 Water bridges: M:W.31, M:F.33 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.10: 18 residues within 4Å: Chain C: L.121, M.124, A.125, F.128, M.129, M.138, G.142, V.145, I.146, I.268, P.270, E.271, F.274, A.277, Y.278, L.294 Chain O: C.160, H.161 10 PLIP interactions: 10 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:F.274, C:A.277, C:L.294 Hydrogen bonds: C:E.271 SMA.31: 20 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, F.178, I.268, P.270, E.271, F.274, A.277, Y.278, L.294 11 PLIP interactions: 11 interactions with chain M Hydrophobic interactions: M:F.128, M:F.128, M:I.146, M:I.164, M:F.178, M:P.270, M:F.274, M:F.274, M:A.277, M:L.294 Hydrogen bonds: M:E.271

2 x UQ: Coenzyme Q10, (2Z,6E,10Z,14E,18E,22E,26Z)-isomer(Non-covalent)

UQ.11: 9 residues within 4Å: Chain C: L.21, S.35, L.197, L.200, H.201, S.205, F.220, D.228 Ligands: HEM.9 3 PLIP interactions: 3 interactions with chain C Hydrophobic interactions: C:L.197 Water bridges: C:S.35 pi-Stacking: C:F.220 UQ.32: 8 residues within 4Å: Chain M: L.21, S.35, L.197, H.201, S.205, F.220, D.228 Ligands: HEM.30 4 PLIP interactions: 4 interactions with chain M Hydrophobic interactions: M:L.197, M:L.197 Water bridges: M:S.35 pi-Stacking: M:F.220

2 x HEC: HEME C(Covalent)

HEC.16: 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, F.153, I.158, G.159, M.160, P.163, I.164, L.190 18 PLIP interactions: 18 interactions with chain D, Hydrophobic interactions: D:V.36, D:N.105, D:A.108, D:P.110, D:P.111, D:I.116, D:F.153, D:I.158, D:M.160, D:P.163, D:I.164, D:L.190 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.35: 19 residues within 4Å: Chain N: V.36, C.37, 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 16 PLIP interactions: 16 interactions with chain N, Hydrophobic interactions: N:V.36, N:N.105, N:A.108, N:P.110, N:P.111, N:I.116, 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-Cation interactions: N:H.41 Metal complexes: N:H.41

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

FES.18: 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.38: 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

4 x CDL: CARDIOLIPIN(Non-covalent)

CDL.21: 20 residues within 4Å: Chain C: S.29, N.32, L.36, K.227, L.230, L.234, L.235 Chain D: Y.220, K.223, R.224, K.231 Chain F: M.70, R.71 Chain G: Y.29, G.33, I.34, N.36, V.37, R.40 Ligands: CDL.22 21 PLIP interactions: 9 interactions with chain D, 6 interactions with chain C, 1 interactions with chain F, 5 interactions with chain G Hydrophobic interactions: D:Y.220, D:Y.220, C:L.36, C:L.234, C:L.234, C:L.235, G:Y.29, G:I.34 Hydrogen bonds: D:K.231, C:N.32, F:M.70, G:N.36 Water bridges: D:K.223, D:K.223, D:R.224, G:R.40 Salt bridges: D:K.223, D:R.224, D:K.231, C:K.227, G:R.40 CDL.22: 9 residues within 4Å: Chain C: S.28, S.29, W.30, F.33 Chain F: Q.72 Chain G: R.40, T.41 Ligands: PEE.12, CDL.21 11 PLIP interactions: 4 interactions with chain C, 2 interactions with chain F, 5 interactions with chain G Hydrophobic interactions: C:W.30 Hydrogen bonds: C:S.29, C:W.30, F:Q.72, F:Q.72 Water bridges: C:S.29, G:R.40, G:R.40 Salt bridges: G:R.40, G:R.40, G:R.40 CDL.36: 26 residues within 4Å: Chain M: S.29, N.32, F.33, L.36, M.89, I.92, K.227, L.230, G.231, L.234, A.238 Chain N: Y.220, K.223, R.224, K.231 Chain P: M.70, R.71, Q.72 Chain Q: Y.29, F.30, G.33, I.34, N.36, V.37, R.40 Ligands: CDL.40 20 PLIP interactions: 6 interactions with chain N, 8 interactions with chain M, 6 interactions with chain Q Hydrogen bonds: N:K.231, M:S.29, M:N.32, Q:N.36 Water bridges: N:K.223, N:R.224, Q:R.40 Salt bridges: N:K.223, N:R.224, N:K.231, Q:R.40 Hydrophobic interactions: M:N.32, M:F.33, M:L.36, M:I.92, M:L.234, M:A.238, Q:Y.29, Q:F.30, Q:I.34 CDL.40: 10 residues within 4Å: Chain M: S.28, S.29, W.30 Chain P: Q.72 Chain Q: V.37, R.40, T.41, C.44 Ligands: PEE.33, CDL.36 11 PLIP interactions: 4 interactions with chain M, 2 interactions with chain P, 5 interactions with chain Q Hydrophobic interactions: M:W.30 Hydrogen bonds: M:S.29, M:S.29, M:W.30, 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

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.
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

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

Related Entries With Identical Sequence