SMTL ID : 7y5a.1

Cryo-EM structure of the Mycolicibacterium smegmatis F1-ATPase

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-3-1-mer

Ligands

3 x ATP: ADENOSINE-5'-TRIPHOSPHATE(Non-covalent)

ATP.1: 13 residues within 4Å: Chain A: D.173, R.174, K.175, T.176, G.177, K.178, T.179, F.360, R.365, Q.433, Q.435 Chain F: Y.372 Ligands: MG.2 10 PLIP interactions: 9 interactions with chain A, 1 interactions with chain F Hydrogen bonds: A:K.175, A:T.176, A:G.177, A:Q.433, A:Q.435, F:Y.372 Salt bridges: A:K.175, A:K.175, A:K.175, A:K.178 ATP.3: 13 residues within 4Å: Chain B: D.173, R.174, K.175, T.176, G.177, K.178, T.179, A.180, F.360, R.365, Q.433, Q.435 Ligands: MG.4 14 PLIP interactions: 14 interactions with chain B Hydrogen bonds: B:K.175, B:T.176, B:G.177, B:K.178, B:T.179, B:T.179, B:A.180, B:Q.433, B:Q.435, B:Q.435 Salt bridges: B:K.175, B:K.178, B:K.178 pi-Cation interactions: B:R.365 ATP.5: 12 residues within 4Å: Chain C: K.175, T.176, G.177, K.178, T.179, F.360, R.365, Q.433, P.434, Q.435 Chain E: D.363 Ligands: MG.6 17 PLIP interactions: 17 interactions with chain C Hydrogen bonds: C:K.175, C:T.176, C:G.177, C:K.178, C:T.179, C:T.179, C:T.179, C:A.180, C:Q.433, C:Q.435 Salt bridges: C:K.175, C:K.175, C:K.175, C:K.178, C:K.178 pi-Cation interactions: C:R.365, C:R.365

5 x MG: MAGNESIUM ION(Non-functional Binders)(Non-covalent)

MG.2: 1 residues within 4Å: Ligands: ATP.1 No protein-ligand interaction detected (PLIP) MG.4: 2 residues within 4Å: Chain B: T.179 Ligands: ATP.3 No protein-ligand interaction detected (PLIP) MG.6: 2 residues within 4Å: Chain C: T.179 Ligands: ATP.5 No protein-ligand interaction detected (PLIP) MG.8: 3 residues within 4Å: Chain D: T.173, R.199 Ligands: ADP.7 1 PLIP interactions: 1 interactions with chain D Metal complexes: D:T.173 MG.10: 4 residues within 4Å: Chain F: G.171, K.172, T.173 Ligands: ADP.9 No protein-ligand interaction detected (PLIP)

2 x ADP: ADENOSINE-5'-DIPHOSPHATE(Non-covalent)

ADP.7: 16 residues within 4Å: Chain A: S.375, R.376 Chain D: G.167, A.168, G.169, V.170, G.171, K.172, T.173, V.174, R.199, F.349, M.422, A.425, F.428 Ligands: MG.8 11 PLIP interactions: 7 interactions with chain D, 4 interactions with chain A Hydrogen bonds: D:G.169, D:V.170, D:G.171, D:K.172, D:T.173, A:S.375, A:R.376, A:R.376 Salt bridges: D:R.199, D:R.199, A:R.376 ADP.9: 13 residues within 4Å: Chain C: S.347, R.376 Chain F: G.169, V.170, G.171, K.172, T.173, R.199, F.349, M.422, A.425, F.428 Ligands: MG.10 10 PLIP interactions: 8 interactions with chain F, 2 interactions with chain C Hydrogen bonds: F:G.169, F:V.170, F:G.171, F:K.172, F:T.173, F:T.173, F:T.173, C:R.376 Salt bridges: F:R.199, C:R.376

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wong, C.F. et al., Structural Elements Involved in ATP Hydrolysis Inhibition and ATP Synthesis of Tuberculosis and Nontuberculous Mycobacterial F-ATP Synthase Decipher New Targets for Inhibitors. Antimicrob.Agents Chemother. (2022)

Release Date

2022-11-23

Peptides

ATP synthase subunit alpha: ABC
ATP synthase subunit beta: DEF
ATP synthase gamma chain: G

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

G
G

ATP synthase subunit alpha

ATP synthase subunit beta

ATP synthase gamma chain

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