SMTL ID : 6haw.1

Crystal structure of bovine cytochrome bc1 in complex with 2-pyrazolyl quinolone inhibitor WDH2G7

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.45 Å

Oligo State

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

Ligands

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

6PE.1: 8 residues within 4Å: Chain A: S.432, F.435, L.437 Chain C: H.220 Chain D: M.221, K.225 Ligands: CDL.6, PX4.24 5 PLIP interactions: 3 interactions with chain A, 2 interactions with chain C Hydrophobic interactions: A:L.437 Hydrogen bonds: A:S.432, A:F.435 Salt bridges: C:H.220, C:H.220

4 x PGE: TRIETHYLENE GLYCOL(Non-functional Binders)

PGE.2: 1 residues within 4Å: Chain A: R.381 No protein-ligand interaction detected (PLIP) PGE.16: 3 residues within 4Å: Chain C: A.16, L.197, H.200 No protein-ligand interaction detected (PLIP) PGE.17: 4 residues within 4Å: Chain C: L.120, I.145, F.273, L.293 No protein-ligand interaction detected (PLIP) PGE.18: 2 residues within 4Å: Chain C: F.127, M.128 No protein-ligand interaction detected (PLIP)

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

PO4.3: 5 residues within 4Å: Chain A: Y.277, G.278, G.279, G.280 Chain B: L.119 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:G.278, A:G.278 PO4.4: 7 residues within 4Å: Chain A: D.325, M.328, F.329, Q.332, P.425, R.429, I.430 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.325, A:M.328, A:Q.332 PO4.5: 7 residues within 4Å: Chain A: D.325, Q.423, L.424, P.425, D.426 Chain C: P.218 Chain G: F.3 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:L.424, A:D.426 PO4.7: 5 residues within 4Å: Chain B: Q.120, P.121, R.124, I.162, G.163 1 PLIP interactions: 1 interactions with chain B Salt bridges: B:R.124 PO4.21: 3 residues within 4Å: Chain D: G.121, E.123, D.124 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:D.124, D:D.124 Salt bridges: D:R.190 PO4.25: 5 residues within 4Å: Chain E: R.15, P.16, E.17 Chain G: R.23 Ligands: PO4.30 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:E.17 PO4.28: 2 residues within 4Å: Chain F: P.41, Y.83 1 PLIP interactions: 1 interactions with chain F Hydrogen bonds: F:Y.83 PO4.29: 6 residues within 4Å: Chain C: V.214 Chain F: E.29, I.37, Y.45, R.48, I.52 2 PLIP interactions: 2 interactions with chain F Hydrogen bonds: F:E.29 Salt bridges: F:R.48 PO4.30: 4 residues within 4Å: Chain G: R.23, A.24, F.25 Ligands: PO4.25 3 PLIP interactions: 3 interactions with chain G Hydrogen bonds: G:A.24, G:F.25, G:F.25 PO4.31: 4 residues within 4Å: Chain G: H.27, Y.28, F.29, S.30 5 PLIP interactions: 5 interactions with chain G Hydrogen bonds: G:H.27, G:Y.28, G:F.29, G:S.30, G:S.30 PO4.32: 3 residues within 4Å: Chain G: A.42, L.45, R.46 1 PLIP interactions: 1 interactions with chain G Salt bridges: G:R.46

4 x CDL: CARDIOLIPIN(Non-covalent)

CDL.6: 10 residues within 4Å: Chain A: F.329, F.435, W.436, L.437, R.438 Chain C: R.4, F.17, I.18, H.220 Ligands: 6PE.1 5 PLIP interactions: 3 interactions with chain C, 2 interactions with chain A Hydrophobic interactions: C:F.17 Salt bridges: C:R.4, C:H.220, A:R.438 Hydrogen bonds: A:L.437 CDL.13: 10 residues within 4Å: Chain C: S.27, S.28, W.29 Chain F: Q.62 Chain G: V.36, R.39, T.40, C.43 Ligands: PEE.14, CDL.22 6 PLIP interactions: 2 interactions with chain C, 4 interactions with chain G Hydrogen bonds: C:S.28, C:S.28 Hydrophobic interactions: G:T.40 Salt bridges: G:R.39, G:R.39, G:R.39 CDL.22: 14 residues within 4Å: Chain C: S.28, N.31, K.226, L.229, G.230 Chain D: Y.219, K.222, R.223, K.230 Chain F: R.61 Chain G: N.35, V.36, R.39 Ligands: CDL.13 10 PLIP interactions: 2 interactions with chain C, 6 interactions with chain D, 2 interactions with chain G Hydrophobic interactions: C:N.31 Salt bridges: C:K.226, D:K.222, D:R.223, D:K.230, G:R.39 Hydrogen bonds: D:R.223, D:K.230, D:K.230, G:N.35 CDL.27: 3 residues within 4Å: Chain E: S.56, S.60, S.63 4 PLIP interactions: 4 interactions with chain E Hydrogen bonds: E:S.56, E:S.60, E:S.63 Salt bridges: E:K.52

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

PG4.8: 5 residues within 4Å: Chain B: I.238, D.354, E.355, S.358 Chain I: R.30 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain I Hydrogen bonds: B:D.354, B:D.354, B:S.358, I:R.30

2 x PX6: 1,2-DIPALMITOYL-SN-GLYCERO-3-PHOSPHATE(Non-covalent)

PX6.9: 5 residues within 4Å: Chain B: K.335, D.377, A.378, V.379, A.380 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:V.379 Salt bridges: B:K.335 PX6.19: 2 residues within 4Å: Chain C: E.110, N.113 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:N.113

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

HEM.10: 20 residues within 4Å: Chain C: Q.43, I.44, G.47, L.48, L.50, A.51, R.79, H.82, A.83, A.86, F.89, T.125, G.129, Y.130, L.132, P.133, F.178, H.181, F.182, P.185 17 PLIP interactions: 17 interactions with chain C, Hydrophobic interactions: C:Q.43, C:I.44, C:L.50, C:A.83, C:A.86, C:F.89, C:T.125, C:L.132, C:L.132, C:F.178, C:F.182, C:F.182 Salt bridges: C:R.79, C:R.79 pi-Stacking: C:H.181 Metal complexes: C:H.82, C:H.181 HEM.11: 22 residues within 4Å: Chain C: W.30, G.33, S.34, L.36, L.93, H.96, V.97, R.99, S.105, F.108, T.111, W.112, G.115, V.116, L.118, L.119, H.195, L.196, L.199, S.204, N.205 Ligands: FX2.15 22 PLIP interactions: 22 interactions with chain C, Hydrophobic interactions: C:L.36, C:L.36, C:L.93, C:V.97, C:T.111, C:W.112, C:W.112, C:L.118, C:L.119, C:L.196, C:L.199 Hydrogen bonds: C:G.33, C:S.105, C:N.205 Water bridges: C:F.32, C:S.204 Salt bridges: C:H.96, C:R.99, C:R.99 pi-Cation interactions: C:R.99 Metal complexes: C:H.96, C:H.195

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

LMT.12: 4 residues within 4Å: Chain C: H.344, T.348, Q.351 Chain G: E.64 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:Q.351

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

PEE.14: 16 residues within 4Å: Chain C: W.29, Y.94, M.95, G.98, Y.102, Y.103, M.315, Q.321, F.324, W.325, V.328, L.331 Chain F: Q.62 Chain G: C.43, V.47 Ligands: CDL.13 9 PLIP interactions: 8 interactions with chain C, 1 interactions with chain F Hydrophobic interactions: C:W.29, C:Y.103, C:F.324, C:V.328, C:L.331 Hydrogen bonds: C:Y.102, C:Y.102, C:Q.321, F:Q.62 PEE.26: 10 residues within 4Å: Chain C: I.77 Chain D: H.199, M.203, K.206, M.207, M.210 Chain E: Y.49, N.53, Q.57 Chain J: D.35 7 PLIP interactions: 2 interactions with chain J, 3 interactions with chain D, 2 interactions with chain E Hydrogen bonds: J:E.31, J:D.35, E:N.53, E:Q.57 Hydrophobic interactions: D:M.210 Salt bridges: D:H.199, D:K.206

1 x FX2: 7-methoxy-3-methyl-2-[1-[[4-(trifluoromethyloxy)phenyl]methyl]pyrazol-4-yl]-3~{H}-quinolin-4-one(Non-covalent)

FX2.15: 11 residues within 4Å: Chain C: A.16, F.17, L.20, I.26, W.30, S.34, I.41, L.196, H.200, F.219 Ligands: HEM.11 5 PLIP interactions: 5 interactions with chain C Hydrophobic interactions: C:F.17, C:L.20, C:I.41, C:L.196 pi-Stacking: C:F.219

1 x HEC: HEME C(Non-covalent)

HEC.20: 20 residues within 4Å: Chain D: V.31, V.35, C.36, C.39, H.40, N.104, A.107, P.109, P.110, I.115, R.119, Y.125, L.129, L.130, F.152, I.157, G.158, M.159, P.162, I.163 15 PLIP interactions: 15 interactions with chain D, Hydrophobic interactions: D:V.31, D:V.35, D:N.104, D:A.107, D:P.109, D:I.115, D:L.129, D:L.130, D:M.159, D:I.163 Hydrogen bonds: D:Y.125, D:Y.125, D:G.158 Salt bridges: D:R.119 Metal complexes: D:H.40

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

FES.23: 8 residues within 4Å: Chain E: C.139, H.141, L.142, C.144, C.158, C.160, H.161, S.163 2 PLIP interactions: 2 interactions with chain E, Metal complexes: E:H.141, E:C.158

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

PX4.24: 10 residues within 4Å: Chain A: D.410, F.435 Chain E: Y.37, T.40, T.44 Chain J: F.13, R.14, T.16, F.19 Ligands: 6PE.1 5 PLIP interactions: 2 interactions with chain A, 2 interactions with chain E, 1 interactions with chain J Salt bridges: A:D.410 pi-Cation interactions: A:F.435, E:Y.37, J:F.19 Hydrogen bonds: E:T.40

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

David Hong, W. et al., Potent Antimalarial 2-Pyrazolyl Quinolonebc1(Qi) Inhibitors with Improved Drug-like Properties. ACS Med Chem Lett (2018)

Release Date

2019-01-16

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