SMTL ID : 4v1f.1

Crystal structure of a mycobacterial ATP synthase rotor ring in complex with Bedaquiline

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.70 Å

Oligo State

homo-9-mer

Ligands

9 x BQ1: Bedaquiline(Non-covalent)

BQ1.1: 4 residues within 4Å: Chain A: G.62, E.65, A.66, F.69 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:E.65, A:A.66, A:F.69, A:F.69 BQ1.2: 10 residues within 4Å: Chain A: L.63, A.66, A.67, I.70 Chain B: G.62, E.65, A.66, Y.68, F.69, L.72 9 PLIP interactions: 8 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:E.65, B:F.69, B:F.69, B:F.69, B:L.72, A:I.70 Water bridges: B:E.65, B:E.65 Salt bridges: B:E.65 BQ1.7: 4 residues within 4Å: Chain C: G.62, E.65, A.66, F.69 4 PLIP interactions: 4 interactions with chain C Hydrophobic interactions: C:E.65, C:A.66, C:F.69, C:F.69 BQ1.9: 4 residues within 4Å: Chain D: G.62, E.65, A.66, F.69 4 PLIP interactions: 4 interactions with chain D Hydrophobic interactions: D:E.65, D:A.66, D:F.69, D:F.69 BQ1.10: 10 residues within 4Å: Chain D: L.63, A.66, A.67, I.70 Chain E: G.62, E.65, A.66, Y.68, F.69, L.72 9 PLIP interactions: 1 interactions with chain D, 8 interactions with chain E Hydrophobic interactions: D:I.70, E:E.65, E:F.69, E:F.69, E:F.69, E:L.72 Water bridges: E:E.65, E:E.65 Salt bridges: E:E.65 BQ1.15: 4 residues within 4Å: Chain F: G.62, E.65, A.66, F.69 4 PLIP interactions: 4 interactions with chain F Hydrophobic interactions: F:E.65, F:A.66, F:F.69, F:F.69 BQ1.17: 4 residues within 4Å: Chain G: G.62, E.65, A.66, F.69 4 PLIP interactions: 4 interactions with chain G Hydrophobic interactions: G:E.65, G:A.66, G:F.69, G:F.69 BQ1.18: 10 residues within 4Å: Chain G: L.63, A.66, A.67, I.70 Chain H: G.62, E.65, A.66, Y.68, F.69, L.72 9 PLIP interactions: 8 interactions with chain H, 1 interactions with chain G Hydrophobic interactions: H:E.65, H:F.69, H:F.69, H:F.69, H:L.72, G:I.70 Water bridges: H:E.65, H:E.65 Salt bridges: H:E.65 BQ1.23: 4 residues within 4Å: Chain I: G.62, E.65, A.66, F.69 4 PLIP interactions: 4 interactions with chain I Hydrophobic interactions: I:E.65, I:A.66, I:F.69, I:F.69

15 x BOG: octyl beta-D-glucopyranoside(Non-covalent)

BOG.3: 10 residues within 4Å: Chain A: G.51, R.52, T.55, I.59 Chain B: L.39, Q.50, F.54, F.57, F.58 Ligands: BOG.6 11 PLIP interactions: 7 interactions with chain B, 4 interactions with chain A Hydrophobic interactions: B:L.39, B:F.54, B:F.54, B:F.54, B:F.57, B:F.58, A:T.55, A:I.59 Hydrogen bonds: B:Q.50, A:G.51 Water bridges: A:T.55 BOG.4: 5 residues within 4Å: Chain A: F.74 Chain B: L.72, A.76, F.80 Ligands: BOG.5 5 PLIP interactions: 4 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:L.72, B:A.76, B:F.80, B:F.80, A:F.74 BOG.5: 6 residues within 4Å: Chain B: A.73, A.76, L.77, F.80, A.81 Ligands: BOG.4 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:A.73, B:A.76, B:A.81 BOG.6: 3 residues within 4Å: Chain A: I.59 Chain B: F.58 Ligands: BOG.3 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:F.58, B:F.58, A:I.59 BOG.8: 7 residues within 4Å: Chain B: T.55, I.59, L.63 Chain C: Q.50, G.51, F.54, F.58 5 PLIP interactions: 2 interactions with chain B, 3 interactions with chain C Hydrophobic interactions: B:I.59, B:L.63, C:F.58, C:F.58 Hydrogen bonds: C:Q.50 BOG.11: 10 residues within 4Å: Chain D: G.51, R.52, T.55, I.59 Chain E: L.39, Q.50, F.54, F.57, F.58 Ligands: BOG.14 11 PLIP interactions: 7 interactions with chain E, 4 interactions with chain D Hydrophobic interactions: E:L.39, E:F.54, E:F.54, E:F.54, E:F.57, E:F.58, D:T.55, D:I.59 Hydrogen bonds: E:Q.50, D:G.51 Water bridges: D:T.55 BOG.12: 5 residues within 4Å: Chain D: F.74 Chain E: L.72, A.76, F.80 Ligands: BOG.13 5 PLIP interactions: 4 interactions with chain E, 1 interactions with chain D Hydrophobic interactions: E:L.72, E:A.76, E:F.80, E:F.80, D:F.74 BOG.13: 6 residues within 4Å: Chain E: A.73, A.76, L.77, F.80, A.81 Ligands: BOG.12 3 PLIP interactions: 3 interactions with chain E Hydrophobic interactions: E:A.73, E:A.76, E:A.81 BOG.14: 3 residues within 4Å: Chain D: I.59 Chain E: F.58 Ligands: BOG.11 3 PLIP interactions: 2 interactions with chain E, 1 interactions with chain D Hydrophobic interactions: E:F.58, E:F.58, D:I.59 BOG.16: 7 residues within 4Å: Chain E: T.55, I.59, L.63 Chain F: Q.50, G.51, F.54, F.58 5 PLIP interactions: 3 interactions with chain F, 2 interactions with chain E Hydrophobic interactions: F:F.58, F:F.58, E:I.59, E:L.63 Hydrogen bonds: F:Q.50 BOG.19: 10 residues within 4Å: Chain G: G.51, R.52, T.55, I.59 Chain H: L.39, Q.50, F.54, F.57, F.58 Ligands: BOG.22 11 PLIP interactions: 4 interactions with chain G, 7 interactions with chain H Hydrophobic interactions: G:T.55, G:I.59, H:L.39, H:F.54, H:F.54, H:F.54, H:F.57, H:F.58 Hydrogen bonds: G:G.51, H:Q.50 Water bridges: G:T.55 BOG.20: 5 residues within 4Å: Chain G: F.74 Chain H: L.72, A.76, F.80 Ligands: BOG.21 5 PLIP interactions: 4 interactions with chain H, 1 interactions with chain G Hydrophobic interactions: H:L.72, H:A.76, H:F.80, H:F.80, G:F.74 BOG.21: 6 residues within 4Å: Chain H: A.73, A.76, L.77, F.80, A.81 Ligands: BOG.20 3 PLIP interactions: 3 interactions with chain H Hydrophobic interactions: H:A.73, H:A.76, H:A.81 BOG.22: 3 residues within 4Å: Chain G: I.59 Chain H: F.58 Ligands: BOG.19 3 PLIP interactions: 1 interactions with chain G, 2 interactions with chain H Hydrophobic interactions: G:I.59, H:F.58, H:F.58 BOG.24: 7 residues within 4Å: Chain H: T.55, I.59, L.63 Chain I: Q.50, G.51, F.54, F.58 5 PLIP interactions: 2 interactions with chain H, 3 interactions with chain I Hydrophobic interactions: H:I.59, H:L.63, I:F.58, I:F.58 Hydrogen bonds: I:Q.50

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Preiss, L. et al., Structure of the mycobacterial ATP synthase Fo rotor ring in complex with the anti-TB drug bedaquiline. Sci Adv (2015)

Release Date

2015-05-20

Peptides

F0F1 ATP SYNTHASE SUBUNIT C: ABCDEFGHI

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
A

E
B

F
C

G
A

H
B

I
C

Membrane

We predict this structure to be a membrane protein.
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F0F1 ATP SYNTHASE SUBUNIT C

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