SMTL ID : 8zi3.1

Cryo-EM reveals transition states of the Acinetobacter baumannii F1-ATPase rotary subunits gamma and epsilon and novel compound targets - Conformation 4

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-3-3-1-mer

Ligands

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

ATP.1: 12 residues within 4Å: Chain B: Q.173, T.174, G.175, K.176, T.177, A.178, F.361, R.366, Q.434, K.435, Q.436 Ligands: MG.2 12 PLIP interactions: 12 interactions with chain B Hydrogen bonds: B:Q.173, B:Q.173, B:T.174, B:G.175, B:K.176, B:T.177, B:A.178, B:Q.434, B:Q.436 Salt bridges: B:K.176, B:K.176 pi-Cation interactions: B:R.366 ATP.4: 13 residues within 4Å: Chain C: Q.173, T.174, G.175, K.176, T.177, A.178, F.361, R.366, Q.434, K.435, Q.436 Chain G: Y.359 Ligands: MG.3 15 PLIP interactions: 14 interactions with chain C, 1 interactions with chain G Hydrogen bonds: C:Q.173, C:Q.173, C:T.174, C:G.175, C:K.176, C:T.177, C:A.178, C:Q.434, C:Q.436, C:Q.436, G:Y.359 Salt bridges: C:K.176, C:K.176 pi-Cation interactions: C:R.366, C:R.366 ATP.11: 14 residues within 4Å: Chain E: R.347 Chain H: R.172, Q.173, T.174, G.175, K.176, T.177, A.178, F.361, R.366, P.367, Q.434, Q.436 Ligands: MG.10 12 PLIP interactions: 11 interactions with chain H, 1 interactions with chain E Hydrogen bonds: H:Q.173, H:T.174, H:G.175, H:K.176, H:T.177, H:T.177, H:A.178, H:Q.434, H:Q.436 Salt bridges: H:K.176, H:K.176, E:R.347

5 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 2 residues within 4Å: Chain B: T.177 Ligands: ATP.1 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:T.177 MG.3: 2 residues within 4Å: Chain C: T.177 Ligands: ATP.4 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:T.177 MG.6: 2 residues within 4Å: Chain D: K.154 Ligands: ADP.5 No protein-ligand interaction detected (PLIP) MG.7: 4 residues within 4Å: Chain G: T.155, E.180 Ligands: ADP.8, PO4.9 2 PLIP interactions: 2 interactions with chain G Metal complexes: G:T.155, G:E.180 MG.10: 2 residues within 4Å: Chain H: T.177 Ligands: ATP.11 1 PLIP interactions: 1 interactions with chain H Metal complexes: H:T.177

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

ADP.5: 12 residues within 4Å: Chain C: S.376, R.377 Chain D: G.151, V.152, G.153, K.154, T.155, V.156, Y.336, A.412, F.415 Ligands: MG.6 12 PLIP interactions: 10 interactions with chain D, 2 interactions with chain C Hydrogen bonds: D:G.151, D:V.152, D:G.153, D:K.154, D:T.155, D:T.155, D:V.156 Salt bridges: D:K.154, C:R.377, C:R.377 pi-Stacking: D:Y.336, D:Y.336 ADP.8: 18 residues within 4Å: Chain G: G.149, G.151, V.152, G.153, K.154, T.155, V.156, N.157, R.181, Y.336, F.409, A.412, F.415 Chain H: V.375, S.376, R.377 Ligands: MG.7, PO4.9 15 PLIP interactions: 3 interactions with chain H, 12 interactions with chain G Hydrogen bonds: H:S.376, G:G.151, G:V.152, G:G.153, G:K.154, G:T.155, G:T.155, G:T.155, G:V.156, G:N.157, G:R.181 Salt bridges: H:R.377, H:R.377, G:K.154 pi-Stacking: G:Y.336

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

PO4.9: 9 residues within 4Å: Chain G: A.150, G.151, K.154, E.180, R.181 Chain H: S.348, R.377 Ligands: MG.7, ADP.8 5 PLIP interactions: 4 interactions with chain G, 1 interactions with chain H Hydrogen bonds: G:G.151, G:E.180 Salt bridges: G:K.154, G:R.181, H:R.377

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Le, K.C.M. et al., Cryo-EM reveals transition states of the Acinetobacter baumannii F 1 -ATPase rotary subunits gamma and epsilon , unveiling novel compound targets. Faseb J. (2024)

Release Date

2024-11-13

Peptides

ATP synthase epsilon chain: A
ATP synthase subunit alpha: BCH
ATP synthase subunit beta: DEG
ATP synthase gamma chain: F

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
e

B
B

C
C

H
A

D
D

E
F

G
E

F
g

ATP synthase epsilon chain

ATP synthase subunit alpha

ATP synthase subunit beta

ATP synthase gamma chain

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