SMTL ID : 8zi0.1

Cryo-EM reveals transition states of the Acinetobacter baumannii F1-ATPase rotary subunits gamma and epsilon and novel compound targets - Conformation 1

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-3-1-1-mer

Ligands

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

ATP.1: 16 residues within 4Å: Chain A: R.172, Q.173, T.174, G.175, K.176, T.177, A.178, Q.201, D.262, F.361, R.366, Q.434, K.435, Q.436 Chain F: R.347 Ligands: MG.2 14 PLIP interactions: 12 interactions with chain A, 2 interactions with chain F Hydrogen bonds: A:Q.173, A:T.174, A:G.175, A:K.176, A:T.177, A:T.177, A:Q.201, A:D.262, A:Q.434, F:R.347 Salt bridges: A:K.176, A:K.176, A:K.176, F:R.347 ATP.3: 16 residues within 4Å: Chain B: R.172, Q.173, T.174, G.175, K.176, T.177, E.332, F.361, R.366, P.367, Q.434, K.435, Q.436 Chain E: R.347, D.350 Ligands: MG.4 13 PLIP interactions: 10 interactions with chain B, 3 interactions with chain E Hydrogen bonds: B:Q.173, B:T.174, B:G.175, B:K.176, B:T.177, B:E.332, B:E.332, B:Q.434, E:D.350 Salt bridges: B:K.176, B:K.176, E:R.347, E:R.347 ATP.6: 15 residues within 4Å: Chain C: Q.173, T.174, G.175, K.176, T.177, A.178, Q.201, D.262, D.263, F.361, R.366, Q.434, Q.436 Chain D: Y.359 Ligands: MG.5 9 PLIP interactions: 9 interactions with chain C Hydrogen bonds: C:Q.173, C:T.174, C:G.175, C:K.176, C:T.177, C:A.178, C:Q.201, C:D.262, C:Q.434

4 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: Q.201 Ligands: ATP.3 No protein-ligand interaction detected (PLIP) MG.5: 3 residues within 4Å: Chain C: T.177, D.262 Ligands: ATP.6 2 PLIP interactions: 2 interactions with chain C Metal complexes: C:T.177, C:D.262 MG.7: 3 residues within 4Å: Chain D: A.150, K.154 Ligands: ADP.8 No protein-ligand interaction detected (PLIP)

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

ADP.8: 11 residues within 4Å: Chain A: S.376, R.377 Chain D: G.151, V.152, G.153, K.154, T.155, V.156, Y.336, F.415 Ligands: MG.7 13 PLIP interactions: 3 interactions with chain A, 10 interactions with chain D Hydrogen bonds: A:S.376, D:G.151, D:V.152, D:G.153, D:K.154, D:T.155, D:V.156, D:Y.336 Salt bridges: A:R.377, A:R.377, D:K.154 pi-Stacking: D:Y.336, D:Y.336

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

PO4.9: 4 residues within 4Å: Chain C: R.377 Chain E: G.149, A.150, Y.302 2 PLIP interactions: 1 interactions with chain E, 1 interactions with chain C Hydrogen bonds: E:A.150 Salt bridges: C: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 subunit alpha: ABC
ATP synthase subunit beta: DEF
ATP synthase epsilon chain: G
ATP synthase gamma chain: H

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

G
e

H
g

ATP synthase subunit alpha

ATP synthase subunit beta

ATP synthase epsilon chain

ATP synthase gamma chain

Related Entries With Identical Sequence