SMTL ID : 5knc.1

Crystal structure of the 3 ADP-bound V1 complex

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.02 Å

Oligo State

hetero-3-3-1-1-mer

Ligands

3 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 5 residues within 4Å: Chain A: T.246, E.272 Chain D: R.357 Ligands: SO4.2, ADP.3 3 PLIP interactions: 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:T.246, H2O.1, H2O.1 MG.10: 4 residues within 4Å: Chain B: T.246, E.268, R.269 Ligands: ADP.11 5 PLIP interactions: 1 interactions with chain B, 4 Ligand-Water interactions Metal complexes: B:T.246, H2O.1, H2O.1, H2O.1, H2O.1 MG.17: 4 residues within 4Å: Chain C: T.246, E.268, R.269 Ligands: ADP.18 4 PLIP interactions: 1 interactions with chain C, 3 Ligand-Water interactions Metal complexes: C:T.246, H2O.2, H2O.2, H2O.2

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

SO4.2: 10 residues within 4Å: Chain A: P.240, F.241, K.245, T.246, R.269, R.340, S.398 Chain D: R.357 Ligands: MG.1, ADP.3 8 PLIP interactions: 6 interactions with chain A, 2 interactions with chain D Hydrogen bonds: A:S.398 Water bridges: A:R.340, A:R.340, D:R.357 Salt bridges: A:K.245, A:R.269, A:R.340, D:R.357

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

ADP.3: 16 residues within 4Å: Chain A: P.240, 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 D: R.357 Ligands: MG.1, SO4.2 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 Salt bridges: A:K.245, D:R.357 pi-Stacking: A:F.432 ADP.11: 16 residues within 4Å: Chain B: P.240, F.241, G.242, A.243, G.244, K.245, T.246, V.247, E.272, F.432, Q.510, N.511, A.512, F.513 Chain E: R.357 Ligands: MG.10 18 PLIP interactions: 14 interactions with chain B, 4 interactions with chain E Hydrogen bonds: B:G.242, B:A.243, B:G.244, B:K.245, B:T.246, B:T.246, B:T.246, B:V.247, B:Q.510, B:A.512 Water bridges: B:T.246, B:R.269, E:R.357, E:R.357 Salt bridges: B:K.245, E:R.357, E:R.357 pi-Stacking: B:F.432 ADP.18: 20 residues within 4Å: Chain C: P.240, F.241, G.242, A.243, G.244, K.245, T.246, V.247, E.272, F.432, Q.510, N.511, A.512, F.513 Chain F: L.355, S.356, R.357, K.359, D.360 Ligands: MG.17 21 PLIP interactions: 17 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:T.246, C:V.247, C:Q.510, C:A.512, F:K.359, F:D.360 Water bridges: C:K.245, C:E.268, C:R.269 Salt bridges: C:K.245, F:R.357, F:R.357 pi-Stacking: C:F.432, C:F.432

14 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 6 residues within 4Å: Chain A: Y.364, S.367, R.368, E.371 Chain E: E.266 Ligands: GOL.5 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.367, A:R.368 GOL.5: 4 residues within 4Å: Chain A: E.371 Chain E: N.222, P.224 Ligands: GOL.4 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.371 GOL.6: 2 residues within 4Å: Chain A: M.102, N.108 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.108 GOL.7: 5 residues within 4Å: Chain A: Q.32, E.45, M.348, L.352, R.368 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Q.32, A:Q.32, A:R.201, A:R.368 GOL.8: 7 residues within 4Å: Chain A: T.246, H.250, Y.263, E.268, E.272, V.276, D.336 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:H.250, A:Y.263, A:Y.263, A:E.272, A:E.272, A:D.336, A:R.340 Water bridges: A:R.340 GOL.9: 4 residues within 4Å: Chain A: D.423, N.436, W.437, I.438 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.436 GOL.12: 5 residues within 4Å: Chain B: K.231, D.257, D.259, N.287, D.330 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:K.231, B:D.259, B:N.287 GOL.13: 7 residues within 4Å: Chain B: P.240, G.402, I.404, G.421, L.422, N.436, Q.439 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:G.402, B:N.436 GOL.14: 5 residues within 4Å: Chain B: D.423, S.425, N.436, W.437, E.475 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:S.425, B:S.425, B:N.436, B:E.475, B:E.475 GOL.15: 4 residues within 4Å: Chain B: I.404, Q.410 Chain F: D.316, R.338 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:Q.410 GOL.16: 2 residues within 4Å: Chain B: D.514, Y.568 No protein-ligand interaction detected (PLIP) GOL.19: 8 residues within 4Å: Chain C: I.404, Q.410, L.413, Q.439 Chain D: S.160, E.315, D.316, R.338 8 PLIP interactions: 5 interactions with chain D, 3 interactions with chain C Hydrogen bonds: D:S.160, D:E.315, D:D.316, D:R.338, D:R.338, C:Q.410, C:Q.410, C:Q.439 GOL.20: 4 residues within 4Å: Chain A: F.109 Chain D: E.121, E.240, E.245 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:E.121, D:E.121, D:E.240, D:E.245 GOL.21: 7 residues within 4Å: Chain C: E.359, S.400, G.401, D.403 Chain F: R.277, T.319 Chain G: T.15 4 PLIP interactions: 1 interactions with chain F, 3 interactions with chain C Hydrogen bonds: F:R.277, C:E.359, C:D.403, C:D.403

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Suzuki, K. et al., Crystal structures of the ATP-binding and ADP-release dwells of the V1 rotary motor. Nat Commun (2016)

Release Date

2016-11-02

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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