SMTL ID : 8igw.2 (1 other biounit)

Hexameric Ring Complex of Engineered V1-ATPase bound to 4 ADPs: A3(De)3_(ADP)3cat,1non-cat, Hexameric Ring Complex of Engineered V1-ATPase bound to 5 ADPs: A3(De)3_(ADP)3cat,2non-cat

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 4.20 Å

Oligo State

hetero-3-3-mer

Ligands

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

ADP.1: 11 residues within 4Å: Chain A: G.238, A.239, G.240, K.241, T.242, V.243, F.428, N.507, A.508, F.509 Ligands: MG.2 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:F.237, A:A.239, A:G.240, A:K.241, A:T.242, A:V.243, A:N.507, A:A.508 Salt bridges: A:K.241 pi-Stacking: A:F.428 ADP.3: 15 residues within 4Å: Chain B: F.237, G.238, A.239, G.240, K.241, T.242, V.243, E.268, F.428, P.429, Q.506, N.507, A.508, F.509 Ligands: MG.4 9 PLIP interactions: 9 interactions with chain B Hydrogen bonds: B:F.237, B:A.239, B:G.240, B:K.241, B:T.242, B:V.243, B:Q.506, B:A.508 Salt bridges: B:K.241 ADP.5: 15 residues within 4Å: Chain C: F.237, G.238, A.239, G.240, K.241, T.242, V.243, E.268, F.428, Q.506, N.507, A.508, F.509 Chain F: R.350 Ligands: MG.6 12 PLIP interactions: 10 interactions with chain C, 2 interactions with chain F Hydrogen bonds: C:A.239, C:G.240, C:K.241, C:T.242, C:T.242, C:V.243, C:E.268, C:Q.506, C:A.508 Salt bridges: C:K.241, F:R.350, F:R.350 ADP.7: 16 residues within 4Å: Chain C: L.409, R.410, V.412, Y.437, L.439 Chain D: P.153, G.154, A.155, K.157, S.158, E.190, E.248, D.249, T.305, R.331 Ligands: MG.8 11 PLIP interactions: 1 interactions with chain C, 10 interactions with chain D Hydrogen bonds: C:V.412, D:G.154, D:K.157, D:S.158, D:E.190, D:E.248, D:D.249, D:R.331, D:R.331 Salt bridges: D:K.157, D:K.157 ADP.9: 14 residues within 4Å: Chain B: L.409, R.410, V.412, Y.437, L.439 Chain F: P.153, G.154, A.155, K.157, S.158, E.190, E.248, T.305 Ligands: MG.10 6 PLIP interactions: 5 interactions with chain F, 1 interactions with chain B Hydrogen bonds: F:G.154, F:K.157, F:S.158, F:S.158, F:E.190, B:Y.437

5 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 5 residues within 4Å: Chain A: K.241, T.242, E.264, E.268 Ligands: ADP.1 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:E.268 MG.4: 5 residues within 4Å: Chain B: K.241, T.242, E.264, E.268 Ligands: ADP.3 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:T.242, B:E.268 MG.6: 4 residues within 4Å: Chain C: T.242, E.264, E.268 Ligands: ADP.5 2 PLIP interactions: 2 interactions with chain C Metal complexes: C:T.242, C:E.268 MG.8: 4 residues within 4Å: Chain D: S.158, E.190, E.248 Ligands: ADP.7 1 PLIP interactions: 1 interactions with chain D Metal complexes: D:S.158 MG.10: 3 residues within 4Å: Chain F: S.158, E.248 Ligands: ADP.9 2 PLIP interactions: 2 interactions with chain F Metal complexes: F:S.158, F:E.248

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kosugi, T. et al., Design of allosteric sites into rotary motor V 1 -ATPase by restoring lost function of pseudo-active sites. Nat.Chem. (2023)

Release Date

2023-07-12

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
G

B
H

C
I

D
J

E
K

F
L

V-type sodium ATPase catalytic subunit A

V-type sodium ATPase subunit B

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