SMTL ID : 5okd.1

Crystal structure of bovine Cytochrome bc1 in complex with inhibitor SCR0911.

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.10 Å

Oligo State

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

Ligands

3 x PG4: TETRAETHYLENE GLYCOL(Non-functional Binders)

PG4.1: 2 residues within 4Å: Chain A: Y.420, R.422 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.422 PG4.8: 5 residues within 4Å: Chain C: L.121, A.125, I.146, F.274 Ligands: PG4.9 No protein-ligand interaction detected (PLIP) PG4.9: 5 residues within 4Å: Chain C: F.128, I.146, L.150, I.164 Ligands: PG4.8 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:I.146

1 x 6PE: 1,2-DIHEXANOYL-SN-GLYCERO-3-PHOSPHOETHANOLAMINE(Non-covalent)

6PE.2: 9 residues within 4Å: Chain A: S.473, F.476, L.478 Chain C: H.221, T.225, I.226 Chain D: K.310 Ligands: CDL.3, PX4.16 8 PLIP interactions: 1 interactions with chain D, 4 interactions with chain C, 3 interactions with chain A Hydrophobic interactions: D:K.310, C:I.226, A:L.478 Hydrogen bonds: C:T.225, A:S.473, A:F.476 Salt bridges: C:H.221, C:H.221

4 x CDL: CARDIOLIPIN(Non-covalent)

CDL.3: 10 residues within 4Å: Chain A: F.370, F.476, W.477, L.478, R.479 Chain C: R.5, F.18, I.19, H.221 Ligands: 6PE.2 6 PLIP interactions: 4 interactions with chain C, 2 interactions with chain A Hydrophobic interactions: C:F.18, C:I.19 Salt bridges: C:R.5, C:H.221, A:R.479 Hydrogen bonds: A:L.478 CDL.10: 11 residues within 4Å: Chain C: S.28, S.29, W.30, M.96 Chain F: Q.73 Chain G: V.38, R.41, T.42, C.45 Ligands: PEE.11, CDL.14 7 PLIP interactions: 4 interactions with chain G, 2 interactions with chain C, 1 interactions with chain F Hydrophobic interactions: G:T.42 Salt bridges: G:R.41, G:R.41, G:R.41 Hydrogen bonds: C:S.29, C:S.29, F:Q.73 CDL.14: 19 residues within 4Å: Chain C: S.29, L.36, K.227, L.230, G.231, L.234 Chain D: Y.304, K.307, R.308, K.315 Chain F: R.72 Chain G: Y.30, F.31, G.34, I.35, N.37, V.38, R.41 Ligands: CDL.10 12 PLIP interactions: 3 interactions with chain G, 6 interactions with chain D, 3 interactions with chain C Hydrophobic interactions: G:I.35, D:Y.304, C:L.234 Hydrogen bonds: G:N.37, D:K.315, D:K.315, C:N.32 Salt bridges: G:R.41, D:K.307, D:R.308, D:K.315, C:K.227 CDL.19: 7 residues within 4Å: Chain E: K.52, S.56, V.59, S.60, S.63 Chain J: E.33, R.34 4 PLIP interactions: 4 interactions with chain E Hydrogen bonds: E:S.56 Salt bridges: E:K.52, E:K.52, E:K.52

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

HEM.4: 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.84, A.87, F.90, T.126, A.127, G.130, Y.131, L.133, P.134, F.179, H.182, F.183, P.186, E.271, Y.273 22 PLIP interactions: 22 interactions with chain C, Hydrophobic interactions: C:L.41, C:Q.44, C:I.45, C:L.51, C:Y.55, C:A.84, C:F.90, C:T.126, C:A.127, C:L.133, C:L.133, C:F.179, C:F.183, C:F.183 Salt bridges: C:R.80, C:R.80 pi-Stacking: C:H.83, C:H.182, C:H.182, C:H.182 Metal complexes: C:H.83, C:H.182 HEM.5: 24 residues within 4Å: Chain C: W.31, G.34, S.35, L.37, G.38, 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, H.196, L.197, L.200, S.205, N.206 Ligands: 9XE.6 24 PLIP interactions: 24 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:W.113, C:L.120, C:L.197, C:L.200, C:L.200 Hydrogen bonds: C:G.34, C:S.106, C:N.206 Water bridges: C:W.31, C:F.33 Salt bridges: C:H.97, C:R.100, C:R.100 pi-Cation interactions: C:R.100 Metal complexes: C:H.97, C:H.196

1 x 9XE: 7-methoxy-3-methyl-2-[5-[4-(trifluoromethyloxy)phenyl]pyridin-3-yl]-1~{H}-quinolin-4-one(Non-covalent)

9XE.6: 14 residues within 4Å: Chain C: A.17, F.18, L.21, S.35, G.38, I.39, L.197, H.201, S.205, F.220, D.228, I.229, A.232 Ligands: HEM.5 6 PLIP interactions: 6 interactions with chain C Hydrophobic interactions: C:F.18, C:L.21, C:L.197 Hydrogen bonds: C:S.35 pi-Stacking: C:F.18, C:F.220

1 x LMT: DODECYL-BETA-D-MALTOSIDE(Non-covalent)

LMT.7: 5 residues within 4Å: Chain C: H.345, I.348, T.349, Q.352 Chain G: E.66 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:Q.352, C:Q.352

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

PEE.11: 17 residues within 4Å: Chain C: W.30, Y.95, M.96, G.99, R.100, Y.103, Y.104, M.316, Q.322, F.325, W.326, V.329, L.332 Chain F: Q.73 Chain G: C.45, V.49 Ligands: CDL.10 14 PLIP interactions: 13 interactions with chain C, 1 interactions with chain F Hydrophobic interactions: C:W.30, C:W.30, C:W.30, C:Y.103, C:Y.104, C:F.325, C:W.326, C:W.326, C:V.329, C:L.332 Hydrogen bonds: C:Y.103, C:Y.103, C:Q.322, F:Q.73 PEE.18: 18 residues within 4Å: Chain C: I.78, M.82, L.233, I.236, M.240 Chain D: H.284, M.288, K.291, M.292, M.295, M.296 Chain E: Y.49, A.50, A.51, N.53, V.54, Q.57 Chain J: D.37 11 PLIP interactions: 4 interactions with chain E, 3 interactions with chain C, 3 interactions with chain D, 1 interactions with chain J Hydrophobic interactions: E:Y.49, E:A.50, E:V.54, C:L.233, C:I.236, C:I.236, D:M.295 Hydrogen bonds: E:Q.57, J:D.37 Salt bridges: D:H.284, D:K.291

1 x HEC: HEME C(Non-covalent)

HEC.12: 23 residues within 4Å: Chain D: V.116, V.120, C.121, C.124, H.125, N.189, A.192, L.193, P.194, P.195, L.197, I.200, R.204, Y.210, V.211, L.214, L.215, F.237, I.242, G.243, M.244, P.247, I.248 20 PLIP interactions: 20 interactions with chain D, Hydrophobic interactions: D:V.116, D:V.120, D:N.189, D:A.192, D:P.194, D:P.195, D:L.197, D:I.200, D:V.211, D:L.214, D:L.215, D:L.215, D:I.242, D:P.247, D:I.248 Hydrogen bonds: D:Y.210, D:Y.210, D:G.243 Salt bridges: D:R.204 Metal complexes: D:H.125

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

PO4.13: 2 residues within 4Å: Chain D: E.208, R.275 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:E.208 Salt bridges: D:R.275 PO4.17: 5 residues within 4Å: Chain E: R.15, P.16, E.17 Chain G: R.25 Ligands: PO4.21 3 PLIP interactions: 3 interactions with chain E Hydrogen bonds: E:E.17 Water bridges: E:R.15, E:E.17 PO4.20: 2 residues within 4Å: Chain F: P.52, Y.94 1 PLIP interactions: 1 interactions with chain F Hydrogen bonds: F:Y.94 PO4.21: 4 residues within 4Å: Chain G: R.25, A.26, F.27 Ligands: PO4.17 2 PLIP interactions: 2 interactions with chain G Hydrogen bonds: G:A.26, G:F.27 PO4.22: 5 residues within 4Å: Chain G: F.27, H.29, Y.30, F.31, S.32 6 PLIP interactions: 6 interactions with chain G Hydrogen bonds: G:H.29, G:H.29, G:Y.30, G:F.31, G:S.32, G:S.32 PO4.23: 3 residues within 4Å: Chain G: A.44, L.47, R.48 1 PLIP interactions: 1 interactions with chain G Salt bridges: G:R.48

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

FES.15: 9 residues within 4Å: Chain E: C.139, H.141, L.142, C.144, C.158, C.160, H.161, S.163, P.175 3 PLIP interactions: 2 interactions with chain E, 1 Ligand-Water interactions, Metal complexes: E:H.141, E:C.158, H2O.3

1 x PX4: 1,2-DIMYRISTOYL-SN-GLYCERO-3-PHOSPHOCHOLINE(Non-covalent)

PX4.16: 15 residues within 4Å: Chain A: Y.450, D.451, F.476, L.478 Chain D: M.306 Chain E: Y.37, T.40, T.43, T.44, V.47 Chain J: F.15, R.16, T.18, F.21 Ligands: 6PE.2 7 PLIP interactions: 4 interactions with chain E, 2 interactions with chain A, 1 interactions with chain J Hydrophobic interactions: E:T.43, E:V.47 Hydrogen bonds: E:T.40 pi-Cation interactions: E:Y.37, A:F.476, J:F.21 Salt bridges: A:D.451

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Amporndanai, K. et al., X-ray and cryo-EM structures of inhibitor-bound cytochromebc1complexes for structure-based drug discovery. IUCrJ (2018)

Release Date

2018-02-28

Peptides

Cytochrome b-c1 complex subunit 1, mitochondrial: A
Cytochrome b-c1 complex subunit 2, mitochondrial: B
Cytochrome b: C
Cytochrome c1, heme protein, mitochondrial: D
Cytochrome b-c1 complex subunit Rieske, mitochondrial: E
Cytochrome b-c1 complex subunit 7: F
Cytochrome b-c1 complex subunit 8: G
Cytochrome b-c1 complex subunit 6, mitochondrial: H
Cytochrome b-c1 complex subunit Rieske, mitochondrial: I
Cytochrome b-c1 complex subunit 9: J

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

G
G

H
H

I
I

J
J

Membrane

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

Cytochrome b-c1 complex subunit 1, mitochondrial

Cytochrome b-c1 complex subunit 2, mitochondrial

Cytochrome b

Cytochrome c1, heme protein, mitochondrial

Cytochrome b-c1 complex subunit Rieske, mitochondrial

Cytochrome b-c1 complex subunit 7

Cytochrome b-c1 complex subunit 8

Cytochrome b-c1 complex subunit 6, mitochondrial

Cytochrome b-c1 complex subunit Rieske, mitochondrial

Cytochrome b-c1 complex subunit 9

Related Entries With Identical Sequence