SMTL ID : 5hkk.2 (1 other biounit)

Caldalaklibacillus thermarum F1-ATPase (wild type)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 3.00 Å

Oligo State

hetero-oligomer

Ligands

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

ADP.1: 14 residues within 4Å: Chain A: R.171, Q.172, T.173, G.174, K.175, T.176, T.177, F.349, R.354, P.355, Q.422, D.423, E.424 Ligands: MG.2 13 PLIP interactions: 13 interactions with chain A Hydrogen bonds: A:Q.172, A:T.173, A:G.174, A:K.175, A:T.176, A:T.176, A:T.177, A:T.177, A:Q.422, A:E.424 Water bridges: A:K.175, A:T.176 Salt bridges: A:K.175 ADP.3: 12 residues within 4Å: Chain B: Q.172, T.173, G.174, K.175, T.176, T.177, F.349, R.354, Q.422, D.423, E.424 Ligands: MG.4 18 PLIP interactions: 18 interactions with chain B Hydrogen bonds: B:Q.172, B:Q.172, B:Q.172, B:T.173, B:T.173, B:G.174, B:K.175, B:T.176, 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 Salt bridges: B:K.175 pi-Stacking: B:F.349 ADP.5: 15 residues within 4Å: Chain C: D.170, R.171, 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.6 16 PLIP interactions: 15 interactions with chain C, 1 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, C:E.424, F:S.344 Water bridges: C:T.176, C:D.261 Salt bridges: C:K.175 ADP.7: 19 residues within 4Å: Chain C: V.363, S.364, R.365 Chain D: G.152, A.153, G.154, V.155, G.156, K.157, T.158, V.159, E.187, Y.334, Q.405, F.407, A.410, F.413, T.414 Ligands: MG.8 18 PLIP interactions: 2 interactions with chain C, 16 interactions with chain D Salt bridges: C:R.365, C:R.365, D:K.157 Hydrogen bonds: D:G.154, D:V.155, D:G.156, D:K.157, D:T.158, D:V.159, D:R.184, D:Q.405 Water bridges: D:G.152, D:K.157, D:T.158, D:R.184, D:R.184, D:E.187 pi-Stacking: D:Y.334 ADP.9: 12 residues within 4Å: Chain E: G.152, A.153, G.154, V.155, G.156, K.157, T.158, V.159, Y.334, F.407, A.410, T.414 10 PLIP interactions: 10 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 pi-Stacking: E:Y.334, E:Y.334 ADP.11: 14 residues within 4Å: Chain B: V.363, R.365 Chain F: G.152, G.154, V.155, G.156, K.157, T.158, V.159, Y.334, F.407, A.410, T.414 Ligands: MG.12 16 PLIP interactions: 14 interactions with chain F, 2 interactions with chain B Hydrogen bonds: F:G.154, F:V.155, F:G.156, F:K.157, F:T.158, F:V.159 Water bridges: F:T.158, F:T.158, F:L.160, F:R.184, F:Q.405, B:S.336 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: 2 residues within 4Å: Chain A: T.176 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.4: 3 residues within 4Å: Chain B: T.176, D.261 Ligands: ADP.3 5 PLIP interactions: 1 interactions with chain B, 4 Ligand-Water interactions Metal complexes: B:T.176, H2O.1, H2O.1, H2O.1, H2O.1 MG.6: 3 residues within 4Å: Chain C: T.176, D.261 Ligands: ADP.5 5 PLIP interactions: 1 interactions with chain C, 4 Ligand-Water interactions Metal complexes: C:T.176, H2O.2, H2O.2, H2O.2, H2O.2 MG.8: 4 residues within 4Å: Chain D: T.158, E.183, R.184 Ligands: ADP.7 5 PLIP interactions: 1 interactions with chain D, 4 Ligand-Water interactions Metal complexes: D:T.158, H2O.2, H2O.3, H2O.3, H2O.3 MG.12: 4 residues within 4Å: Chain F: T.158, E.183, R.184 Ligands: ADP.11 5 PLIP interactions: 1 interactions with chain F, 4 Ligand-Water interactions Metal complexes: F:T.158, H2O.4, H2O.5, H2O.5, H2O.5 MG.13: 1 residues within 4Å: Ligands: ATP.14 No protein-ligand interaction detected (PLIP)

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

PO4.10: 6 residues within 4Å: Chain A: R.365 Chain E: K.157, R.184, D.245, N.246, R.249 5 PLIP interactions: 4 interactions with chain E, 1 interactions with chain A Hydrogen bonds: 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.14: 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.13 16 PLIP interactions: 13 interactions with chain H, 3 interactions with chain G Hydrogen bonds: H:E.83, H:D.89, H:D.89, H:R.92, H:R.92, H:R.92, G:S.145, G:S.145 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 Water bridges: G:T.147

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
I

B
J

C
K

D
L

E
M

F
N

G
O

H
P

ATP synthase subunit alpha

ATP synthase subunit beta

ATP synthase gamma chain

ATP synthase epsilon chain

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