SMTL ID : 5knb.1

Crystal structure of the 2 ADP-bound V1 complex

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 3.25 Å

Oligo State

hetero-3-3-1-1-mer

Ligands

2 x MG: MAGNESIUM ION(Non-covalent)

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

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

ADP.2: 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.1 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:K.245, B:K.245, E:R.357, E:R.357 Salt bridges: B:K.245, E:R.357, E:R.357 pi-Stacking: B:F.432 ADP.5: 17 residues within 4Å: Chain C: P.240, G.242, A.243, G.244, K.245, T.246, V.247, E.272, F.432, P.433, N.511, A.512, F.513 Chain F: L.355, S.356, R.357 Ligands: MG.4 16 PLIP interactions: 2 interactions with chain F, 14 interactions with chain C Salt bridges: F:R.357, F:R.357, C:K.245 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:A.512 Water bridges: C:R.269, C:R.269 pi-Stacking: C:F.432, C:F.432

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 4 residues within 4Å: Chain B: D.423, S.425, N.436, W.437 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:S.425, B:S.425, B:N.436, B:W.437 GOL.6: 5 residues within 4Å: Chain B: F.109 Chain E: G.120, E.121, E.240, E.245 3 PLIP interactions: 3 interactions with chain E Hydrogen bonds: E:E.121, E:E.240, E:E.240

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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