SMTL ID : 8spx.1

PS3 F1 Rotorless, high ATP

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-3-mer

Ligands

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

ATP.1: 14 residues within 4Å: Chain A: R.146, Q.147, T.148, G.149, K.150, T.151, S.152, F.324, R.329, Q.397, D.398, L.399 Chain D: R.352 Ligands: MG.2 11 PLIP interactions: 11 interactions with chain A Hydrogen bonds: A:Q.147, A:Q.147, A:K.150, A:T.151, A:T.151, A:S.152, A:S.152, A:Q.397, A:L.399 Salt bridges: A:K.150, A:K.150 ATP.3: 14 residues within 4Å: Chain B: R.146, Q.147, T.148, G.149, K.150, T.151, S.152, F.324, R.329, Q.397, D.398, L.399 Chain E: Y.364 Ligands: MG.4 14 PLIP interactions: 13 interactions with chain B, 1 interactions with chain E Hydrogen bonds: B:D.145, B:Q.147, B:Q.147, B:Q.147, B:T.148, B:G.149, B:K.150, B:T.151, B:S.152, B:S.152, B:Q.397, E:Y.364 Salt bridges: B:K.150, B:K.150 ATP.5: 13 residues within 4Å: Chain C: R.146, Q.147, T.148, G.149, K.150, T.151, S.152, F.324, R.329, Q.397, D.398, L.399 Ligands: MG.6 12 PLIP interactions: 12 interactions with chain C Hydrogen bonds: C:Q.147, C:T.148, C:G.149, C:K.150, C:T.151, C:T.151, C:S.152, C:S.152, C:Q.397, C:L.399 Salt bridges: C:K.150, C:K.150 ATP.7: 15 residues within 4Å: Chain C: R.340 Chain D: A.160, G.161, V.162, G.163, K.164, T.165, V.166, R.191, N.253, Y.341, F.414, A.417, F.420 Ligands: MG.8 18 PLIP interactions: 14 interactions with chain D, 4 interactions with chain C Hydrogen bonds: D:G.159, D:G.161, D:V.162, D:G.163, D:K.164, D:T.165, D:V.166, D:R.191, D:N.253, D:N.253, C:R.340 Salt bridges: D:K.164, D:K.164, D:R.191, C:R.340, C:R.340, C:R.340 pi-Stacking: D:Y.341 ATP.9: 18 residues within 4Å: Chain A: S.311, V.338, S.339, R.340 Chain E: A.160, G.161, V.162, G.163, K.164, T.165, V.166, R.191, N.253, Y.341, A.417, F.420, T.421 Ligands: MG.10 16 PLIP interactions: 4 interactions with chain A, 12 interactions with chain E Hydrogen bonds: A:S.339, E:G.161, E:V.162, E:G.163, E:K.164, E:T.165, E:V.166, E:N.253 Salt bridges: A:R.340, A:R.340, A:R.340, E:K.164, E:K.164, E:R.191 pi-Stacking: E:Y.341, E:Y.341

6 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 2 residues within 4Å: Chain A: T.151 Ligands: ATP.1 No protein-ligand interaction detected (PLIP) MG.4: 3 residues within 4Å: Chain B: Q.175, D.236 Ligands: ATP.3 No protein-ligand interaction detected (PLIP) MG.6: 4 residues within 4Å: Chain C: T.151, Q.175, D.236 Ligands: ATP.5 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:T.151 MG.8: 4 residues within 4Å: Chain D: T.165, E.190, R.191 Ligands: ATP.7 1 PLIP interactions: 1 interactions with chain D Metal complexes: D:T.165 MG.10: 3 residues within 4Å: Chain E: T.165, N.253 Ligands: ATP.9 No protein-ligand interaction detected (PLIP) MG.11: 4 residues within 4Å: Chain F: T.165, E.194 Ligands: ADP.12, PO4.13 1 PLIP interactions: 1 interactions with chain F Metal complexes: F:T.165

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

ADP.12: 14 residues within 4Å: Chain B: S.339, R.340, V.341 Chain F: A.160, G.161, V.162, G.163, K.164, T.165, V.166, Y.341, A.417 Ligands: MG.11, PO4.13 11 PLIP interactions: 9 interactions with chain F, 2 interactions with chain B Hydrogen bonds: F:G.161, F:V.162, F:G.163, F:K.164, F:T.165, F:T.165, F:V.166, B:R.340 Salt bridges: F:K.164, B:R.340 pi-Stacking: F:Y.341

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

PO4.13: 9 residues within 4Å: Chain B: R.340 Chain F: K.164, T.165, R.191, E.194, N.253, R.256 Ligands: MG.11, ADP.12 6 PLIP interactions: 5 interactions with chain F, 1 interactions with chain B Hydrogen bonds: F:T.165, F:N.253 Salt bridges: F:K.164, F:R.191, F:R.256, B:R.340

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Sobti, M. et al., The series of conformational states adopted by rotorless F 1 -ATPase during its hydrolysis cycle. Structure (2024)

Release Date

2024-01-24

Peptides

ATP synthase subunit alpha: ABC
ATP synthase subunit beta: DEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

ATP synthase subunit alpha

ATP synthase subunit beta

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