SMTL ID : 7dqe.1

Crystal structure of the ADP-bound mutant A(S23C)3B(N64C)3 complex from enterococcus hirae V-ATPase

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.69 Å

Oligo State

hetero-3-3-mer

Ligands

3 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 3 residues within 4Å: Chain A: T.246 Ligands: ADP.2, SO4.3 3 PLIP interactions: 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:T.246, H2O.1, H2O.1 MG.4: 5 residues within 4Å: Chain B: T.246, R.269, E.272 Chain E: R.357 Ligands: ADP.5 3 PLIP interactions: 1 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:T.246, H2O.2, H2O.2 MG.6: 5 residues within 4Å: Chain C: T.246, E.268, R.269, E.272 Ligands: ADP.7 4 PLIP interactions: 1 interactions with chain C, 3 Ligand-Water interactions Metal complexes: C:T.246, H2O.3, H2O.3, H2O.3

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

ADP.2: 16 residues within 4Å: Chain A: P.240, F.241, G.242, A.243, G.244, K.245, T.246, V.247, F.432, Q.510, N.511, A.512, F.513 Chain D: R.357 Ligands: MG.1, SO4.3 13 PLIP interactions: 12 interactions with chain A, 1 interactions with chain D Hydrogen bonds: A:P.240, A:G.242, A:A.243, A:G.244, A:K.245, A:T.246, A:T.246, A:V.247, A:Q.510, A:A.512, D:R.357 Salt bridges: A:K.245 pi-Stacking: A:F.432 ADP.5: 15 residues within 4Å: Chain B: P.240, G.242, A.243, G.244, K.245, T.246, V.247, F.432, Q.510, N.511, A.512, F.513 Chain E: S.356, R.357 Ligands: MG.4 16 PLIP interactions: 12 interactions with chain B, 4 interactions with chain E Hydrogen bonds: B:P.240, B:G.242, B:A.243, B:G.244, B:K.245, B:T.246, B:T.246, B:V.247, B:Q.510, B:A.512 Salt bridges: B:K.245, E:R.357, E:R.357 pi-Stacking: B:F.432 Water bridges: E:R.357, E:R.357 ADP.7: 18 residues within 4Å: Chain C: P.240, F.241, G.242, A.243, G.244, K.245, T.246, V.247, F.432, P.433, Q.510, N.511, A.512, F.513 Chain F: L.355, R.357, K.359 Ligands: MG.6 19 PLIP interactions: 15 interactions with chain C, 4 interactions with chain F Hydrogen bonds: C:P.240, C:G.242, C:A.243, C:G.244, C:K.245, C:T.246, C:T.246, C:V.247, C:Q.510, C:A.512, F:K.359 Water bridges: C:K.245, C:V.248, C:R.269, F:R.357 Salt bridges: C:K.245, F:R.357, F:R.357 pi-Stacking: C:F.432

1 x SO4: SULFATE ION(Non-functional Binders)

SO4.3: 8 residues within 4Å: Chain A: F.241, K.245, R.269, R.340, S.398 Chain D: R.357 Ligands: MG.1, ADP.2 7 PLIP interactions: 2 interactions with chain D, 5 interactions with chain A Water bridges: D:R.357, A:R.340 Salt bridges: D:R.357, A:K.245, A:R.269, A:R.340 Hydrogen bonds: A:S.398

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Imamura, M. et al., The Combination of High-Speed AFM and X-ray Crystallography Reveals Rotary Catalytic Mechanism of Shaftless V1-ATPase. To Be Published

Release Date

2021-12-29

Peptides

V-type sodium ATPase catalytic subunit A: ABC
V-type sodium ATPase subunit B: DEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

V-type sodium ATPase catalytic subunit A

V-type sodium ATPase subunit B

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