SMTL ID : 7vw7.1

Crystal structure of the 2 ADP-AlF4-bound V1 complex

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.82 Å

Oligo State

hetero-3-3-1-1-mer

Ligands

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 3 residues within 4Å: Chain A: S.79, I.94, Q.95 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.95

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

ADP.2: 16 residues within 4Å: Chain B: P.240, G.242, A.243, G.244, K.245, T.246, V.247, E.272, F.432, P.433, Q.510, N.511, A.512 Chain E: R.357 Ligands: MG.3, ALF.4 13 PLIP interactions: 12 interactions with chain B, 1 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:V.247, B:E.272, B:Q.510, B:A.512, E:R.357 Salt bridges: B:K.245 pi-Stacking: B:F.432 ADP.5: 18 residues within 4Å: Chain C: 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 F: L.355, S.356, R.357, K.359 Ligands: MG.6, ALF.7 14 PLIP interactions: 4 interactions with chain F, 10 interactions with chain C Hydrogen bonds: F:R.357, F:K.359, C:G.242, C:A.243, C:G.244, C:K.245, C:T.246, C:V.247, C:Q.510, C:A.512 Salt bridges: F:R.357, F:R.357, C:K.245 pi-Stacking: C:F.432

2 x MG: MAGNESIUM ION(Non-covalent)

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

2 x ALF: TETRAFLUOROALUMINATE ION(Non-covalent)

ALF.4: 12 residues within 4Å: Chain B: F.241, G.242, K.245, T.246, E.268, R.269, S.398 Chain E: G.327, Y.328, R.357 Ligands: ADP.2, MG.3 No protein-ligand interaction detected (PLIP) ALF.7: 11 residues within 4Å: Chain C: F.241, K.245, T.246, E.268, R.269, S.398 Chain F: G.327, Y.328, R.357 Ligands: ADP.5, MG.6 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Shekhar, M. et al., Revealing a Hidden Intermediate of Rotatory Catalysis with X-ray Crystallography and Molecular Simulations. Acs Cent.Sci. (2022)

Release Date

2022-06-22

Peptides

V-type sodium ATPase catalytic subunit A: ABC
V-type sodium ATPase subunit B: DEF
V-type sodium ATPase subunit D: G
V-type sodium ATPase subunit NtpG (F): 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

V-type sodium ATPase catalytic subunit A

V-type sodium ATPase subunit B

V-type sodium ATPase subunit D

V-type sodium ATPase subunit NtpG (F)

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