SMTL ID : 5hkk.1 (1 other biounit)

Caldalaklibacillus thermarum F1-ATPase (wild type)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 3.00 Å

Oligo State

hetero-3-3-1-1-mer

Ligands

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

ADP.1: 14 residues within 4Å: Chain A: D.170, Q.172, T.173, G.174, K.175, T.176, T.177, F.349, R.354, P.355, Q.422, E.424 Chain D: Y.357 Ligands: MG.2 14 PLIP interactions: 2 interactions with chain D, 12 interactions with chain A Hydrogen bonds: D:S.344, D:Y.357, A:Q.172, A:Q.172, A:T.173, A:G.174, A:G.174, A:K.175, A:T.176, A:T.176, A:T.177, A:Q.422, A:E.424 Salt bridges: A:K.175 ADP.4: 14 residues within 4Å: Chain B: D.170, Q.172, T.173, G.174, K.175, T.176, T.177, F.349, R.354, Q.422, D.423, E.424 Chain E: R.345 Ligands: MG.5 17 PLIP interactions: 17 interactions with chain B Hydrogen bonds: B:Q.172, B:Q.172, B:T.173, B:T.173, B:G.174, B:K.175, B:T.176, B:T.177, B:T.177, B:R.354, B:Q.422, B:E.424, B:E.424 Water bridges: B:T.176, B:T.176 Salt bridges: B:K.175 pi-Stacking: B:F.349 ADP.6: 14 residues within 4Å: Chain C: D.170, Q.172, T.173, G.174, K.175, T.176, T.177, F.349, R.354, P.355, Q.422, E.424 Chain F: Y.357 Ligands: MG.7 16 PLIP interactions: 14 interactions with chain C, 2 interactions with chain F Hydrogen bonds: C:D.170, C:Q.172, C:T.173, C:T.173, C:G.174, C:K.175, C:T.176, C:T.177, C:T.177, C:Q.422, C:E.424, F:R.345, F:Y.357 Water bridges: C:T.176 Salt bridges: C:K.175 pi-Stacking: C:F.349 ADP.8: 18 residues within 4Å: Chain C: V.363, S.364, R.365 Chain D: G.152, G.154, V.155, G.156, K.157, T.158, V.159, R.184, E.187, Y.334, F.407, A.410, F.413, T.414 Ligands: MG.9 21 PLIP interactions: 18 interactions with chain D, 3 interactions with chain C Hydrogen bonds: D:G.152, D:G.154, D:V.155, D:G.156, D:K.157, D:T.158, D:T.158, D:V.159, D:Q.405, C:S.364 Water bridges: D:K.157, D:T.158, D:R.184, D:R.184, D:R.184, D:R.184 Salt bridges: D:K.157, D:R.184, C:R.365, C:R.365 pi-Stacking: D:Y.334 ADP.10: 9 residues within 4Å: Chain E: G.152, G.154, V.155, G.156, K.157, T.158, V.159, Y.334, F.407 12 PLIP interactions: 12 interactions with chain E Hydrogen bonds: E:G.154, E:V.155, E:G.156, E:K.157, E:T.158, E:T.158, E:T.158, E:V.159 Water bridges: E:Q.405, E:F.407 pi-Stacking: E:Y.334, E:Y.334 ADP.12: 14 residues within 4Å: Chain B: V.363, R.365 Chain F: A.153, G.154, V.155, G.156, K.157, T.158, V.159, Y.334, F.407, A.410, T.414 Ligands: MG.13 18 PLIP interactions: 16 interactions with chain F, 2 interactions with chain B Hydrogen bonds: F:G.152, F:G.154, F:V.155, F:G.156, F:K.157, F:T.158, F:V.159, B:R.365 Water bridges: F:K.157, F:K.157, F:L.160, F:R.184, F:R.184, F:R.184 Salt bridges: F:K.157, B:R.365 pi-Stacking: F:Y.334, F:Y.334

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

MG.2: 3 residues within 4Å: Chain A: T.176, D.261 Ligands: ADP.1 5 PLIP interactions: 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:T.176, H2O.1, H2O.1, H2O.1, H2O.1 MG.5: 2 residues within 4Å: Chain B: T.176 Ligands: ADP.4 5 PLIP interactions: 1 interactions with chain B, 4 Ligand-Water interactions Metal complexes: B:T.176, H2O.1, H2O.2, H2O.2, H2O.2 MG.7: 3 residues within 4Å: Chain C: T.176, D.261 Ligands: ADP.6 5 PLIP interactions: 1 interactions with chain C, 4 Ligand-Water interactions Metal complexes: C:T.176, H2O.2, H2O.3, H2O.3, H2O.3 MG.9: 4 residues within 4Å: Chain D: T.158, E.183, R.184 Ligands: ADP.8 5 PLIP interactions: 1 interactions with chain D, 4 Ligand-Water interactions Metal complexes: D:T.158, H2O.3, H2O.3, H2O.3, H2O.4 MG.13: 4 residues within 4Å: Chain F: T.158, E.183, R.184 Ligands: ADP.12 5 PLIP interactions: 1 interactions with chain F, 4 Ligand-Water interactions Metal complexes: F:T.158, H2O.5, H2O.5, H2O.6, H2O.6 MG.14: 1 residues within 4Å: Ligands: ATP.15 No protein-ligand interaction detected (PLIP)

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 9 residues within 4Å: Chain A: G.282, R.283, Y.286, P.287, G.288, Y.329 Chain E: S.255, E.256, G.269 6 PLIP interactions: 3 interactions with chain A, 3 interactions with chain E Hydrogen bonds: A:R.283, A:Y.286, A:Y.329, E:S.255 Water bridges: E:S.255, E:S.255

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

PO4.11: 6 residues within 4Å: Chain A: R.365 Chain E: K.157, R.184, D.245, N.246, R.249 6 PLIP interactions: 5 interactions with chain E, 1 interactions with chain A Hydrogen bonds: E:D.245, E:N.246 Salt bridges: E:K.157, E:R.184, E:R.249, A:R.365

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

ATP.15: 14 residues within 4Å: Chain G: S.145, T.147 Chain H: T.81, E.83, E.87, I.88, D.89, R.92, A.93, A.96, R.99, R.123, R.127 Ligands: MG.14 18 PLIP interactions: 15 interactions with chain H, 3 interactions with chain G Hydrogen bonds: H:T.81, H:D.89, H:D.89, H:R.92, H:R.92, H:R.92, G:S.145, G:S.145 Water bridges: H:R.123, H:R.123, G:T.147 Salt bridges: H:R.92, H:R.99, H:R.123, H:R.123, H:R.127, H:R.127 pi-Cation interactions: H:R.92

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ferguson, S.A. et al., Regulation of the thermoalkaliphilic F1-ATPase from Caldalkalibacillus thermarum. Proc.Natl.Acad.Sci.USA (2016)

Release Date

2016-09-21

Peptides

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

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

G
G

H
H

ATP synthase subunit alpha

ATP synthase subunit beta

ATP synthase gamma chain

ATP synthase epsilon chain

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