SMTL ID : 5ze9.1

Crystal structure of AMP-PNP bound mutant A3B3 complex from Enterococcus hirae V-ATPase

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

hetero-3-3-mer

Ligands

3 x ANP: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER(Non-covalent)

ANP.1: 21 residues within 4Å: Chain A: P.240, F.241, G.242, A.243, G.244, K.245, T.246, V.247, E.268, R.269, F.432, Q.510, N.511, A.512, F.513 Chain D: G.327, Y.328, L.355, R.357 Ligands: MG.2, GOL.5 19 PLIP interactions: 15 interactions with chain A, 4 interactions with chain D Hydrogen bonds: A:G.242, A:A.243, A:G.244, A:K.245, A:K.245, A:T.246, A:T.246, A:V.247, A:R.269, A:R.269, A:Q.510, A:A.512, D:R.357, D:R.357 Water bridges: A:K.245, D:K.359 pi-Stacking: A:F.432, A:F.513 Salt bridges: D:R.357 ANP.10: 22 residues within 4Å: Chain B: P.240, F.241, G.242, A.243, G.244, K.245, T.246, V.247, E.268, R.269, F.432, Q.510, N.511, A.512, F.513 Chain E: G.327, Y.328, L.355, R.357, K.359 Ligands: MG.11, GOL.19 27 PLIP interactions: 18 interactions with chain B, 9 interactions with chain E Hydrogen bonds: B:G.242, B:A.243, B:G.244, B:K.245, B:K.245, B:K.245, B:T.246, B:V.247, B:R.269, B:R.269, B:Q.510, B:A.512, E:Y.328, E:R.357, E:R.357, E:K.359 Water bridges: B:T.246, B:T.246, B:E.268, B:R.340, B:R.340, E:S.356, E:R.357, E:K.359, E:D.360 pi-Stacking: B:F.432 Salt bridges: E:R.357 ANP.22: 22 residues within 4Å: Chain C: P.240, F.241, G.242, A.243, G.244, K.245, T.246, V.247, E.268, R.269, F.432, Q.510, N.511, A.512, F.513 Chain F: G.327, Y.328, L.355, R.357, K.359 Ligands: MG.23, GOL.46 26 PLIP interactions: 8 interactions with chain F, 18 interactions with chain C Hydrogen bonds: F:Y.328, F:R.357, F:R.357, F:K.359, C:G.242, C:A.243, C:G.244, C:K.245, C:K.245, C:K.245, C:K.245, C:T.246, C:V.247, C:R.269, C:R.269, C:Q.510, C:A.512 Water bridges: F:S.356, F:K.359, F:K.359, C:T.246, C:T.246, C:T.246, C:E.268 Salt bridges: F:R.357 pi-Stacking: C:F.432

3 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 4 residues within 4Å: Chain A: T.246, R.269, E.272 Ligands: ANP.1 4 PLIP interactions: 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:T.246, H2O.1, H2O.3, H2O.4 MG.11: 3 residues within 4Å: Chain B: T.246, R.269 Ligands: ANP.10 4 PLIP interactions: 1 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:T.246, H2O.9, H2O.9, H2O.11 MG.23: 3 residues within 4Å: Chain C: T.246, D.336 Ligands: ANP.22 4 PLIP interactions: 1 interactions with chain C, 3 Ligand-Water interactions Metal complexes: C:T.246, H2O.20, H2O.21, H2O.21

39 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 6 residues within 4Å: Chain A: Q.57, R.201, E.311, M.348, Y.364, R.368 Ligand excluded by PLIP GOL.4: 5 residues within 4Å: Chain A: Y.364, R.368 Chain E: G.20, P.21, E.266 Ligand excluded by PLIP GOL.5: 6 residues within 4Å: Chain A: T.246, E.272, F.513 Chain D: R.357 Ligands: ANP.1, GOL.7 Ligand excluded by PLIP GOL.6: 4 residues within 4Å: Chain A: L.426, N.436, W.437, I.438 Ligand excluded by PLIP GOL.7: 8 residues within 4Å: Chain A: V.247, H.250, Q.251, K.254, D.275, A.512, F.513 Ligands: GOL.5 Ligand excluded by PLIP GOL.8: 6 residues within 4Å: Chain A: R.430 Chain D: L.145, N.146, S.354, N.377, F.380 Ligand excluded by PLIP GOL.9: 3 residues within 4Å: Chain A: F.109 Chain D: E.121, E.245 Ligand excluded by PLIP GOL.12: 6 residues within 4Å: Chain B: D.423, S.425, L.426, N.436, W.437, E.475 Ligand excluded by PLIP GOL.13: 5 residues within 4Å: Chain B: L.413, Q.439, Y.441 Chain F: R.338, K.342 Ligand excluded by PLIP GOL.14: 6 residues within 4Å: Chain B: H.250, Q.251, K.254, A.512, F.513 Ligands: GOL.19 Ligand excluded by PLIP GOL.15: 5 residues within 4Å: Chain B: N.160, K.197, W.198, P.199, R.202 Ligand excluded by PLIP GOL.16: 5 residues within 4Å: Chain B: F.419, G.421, L.422, D.423, N.436 Ligand excluded by PLIP GOL.17: 8 residues within 4Å: Chain B: F.241, G.242, A.243, S.424, Q.428 Chain E: Q.333, P.353, L.355 Ligand excluded by PLIP GOL.18: 6 residues within 4Å: Chain B: I.47, E.48, E.354, Y.364, R.368 Chain F: G.20 Ligand excluded by PLIP GOL.19: 7 residues within 4Å: Chain B: T.246, V.247, H.250, F.513 Chain E: R.357 Ligands: ANP.10, GOL.14 Ligand excluded by PLIP GOL.20: 4 residues within 4Å: Chain B: V.277, N.278, E.282 Chain E: R.299 Ligand excluded by PLIP GOL.21: 5 residues within 4Å: Chain B: M.102, E.103, Q.106, S.107, N.108 Ligand excluded by PLIP GOL.24: 5 residues within 4Å: Chain C: F.419, G.421, L.422, D.423, N.436 Ligand excluded by PLIP GOL.25: 7 residues within 4Å: Chain C: D.423, S.425, L.426, N.436, W.437, I.438, E.475 Ligand excluded by PLIP GOL.26: 2 residues within 4Å: Chain C: Y.441, L.443 Ligand excluded by PLIP GOL.27: 7 residues within 4Å: Chain C: E.61 Chain F: E.34, N.119, R.233, N.287, T.290 Ligands: GOL.40 Ligand excluded by PLIP GOL.28: 6 residues within 4Å: Chain C: I.404, Q.410, L.413, F.419, Q.439, Y.441 Ligand excluded by PLIP GOL.29: 7 residues within 4Å: Chain C: V.247, H.250, Q.251, K.254, D.275, F.513 Ligands: GOL.46 Ligand excluded by PLIP GOL.30: 6 residues within 4Å: Chain C: S.88, Q.89, M.90, D.99, V.277 Chain F: I.126 Ligand excluded by PLIP GOL.31: 6 residues within 4Å: Chain C: W.255, L.283, I.284, D.285, E.290, L.292 Ligand excluded by PLIP GOL.33: 4 residues within 4Å: Chain D: G.344, Q.346, N.421, G.423 Ligand excluded by PLIP GOL.34: 5 residues within 4Å: Chain A: N.304 Chain D: N.119, G.120, E.121, T.290 Ligand excluded by PLIP GOL.35: 5 residues within 4Å: Chain D: Q.378, Y.408, E.448, K.450, R.451 Ligand excluded by PLIP GOL.36: 7 residues within 4Å: Chain B: N.304 Chain E: N.119, G.120, E.121, V.122, T.290, R.294 Ligand excluded by PLIP GOL.37: 6 residues within 4Å: Chain B: F.109 Chain E: L.116, E.121, E.240, Y.241, E.245 Ligand excluded by PLIP GOL.38: 6 residues within 4Å: Chain E: Q.85, L.86, G.87, L.100, G.101, Y.115 Ligand excluded by PLIP GOL.39: 5 residues within 4Å: Chain A: I.404, Q.410, L.413, Q.439 Chain E: R.338 Ligand excluded by PLIP GOL.40: 7 residues within 4Å: Chain C: E.61, N.304 Chain F: N.119, V.122, T.290, R.294 Ligands: GOL.27 Ligand excluded by PLIP GOL.41: 4 residues within 4Å: Chain F: L.178, G.366, K.367, T.368 Ligand excluded by PLIP GOL.42: 7 residues within 4Å: Chain F: L.86, G.87, F.97, G.101, P.103, I.110, P.112 Ligand excluded by PLIP GOL.43: 4 residues within 4Å: Chain F: I.93, D.183, R.213, M.248 Ligand excluded by PLIP GOL.44: 4 residues within 4Å: Chain C: F.109 Chain F: Y.244, E.245, L.301 Ligand excluded by PLIP GOL.45: 4 residues within 4Å: Chain C: G.350 Chain F: R.271, R.272, E.273 Ligand excluded by PLIP GOL.46: 6 residues within 4Å: Chain C: T.246, H.250, F.513 Chain F: R.357 Ligands: ANP.22, GOL.29 Ligand excluded by PLIP

1 x MES: 2-(N-MORPHOLINO)-ETHANESULFONIC ACID(Non-covalent)

MES.32: 2 residues within 4Å: Chain D: Y.425, T.426 1 PLIP interactions: 1 interactions with chain D Water bridges: D:N.427

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Maruyama, S. et al., Metastable asymmetrical structure of a shaftless V1motor. Sci Adv (2019)

Release Date

2019-02-06

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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