SMTL ID : 5xmi.1

Cryo-EM Structure of the ATP-bound VPS4 mutant-E233Q hexamer (masked)

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY 3.90 Å

Oligo State

homo-hexamer

Ligands

5 x ATP: ADENOSINE-5'-TRIPHOSPHATE(Non-covalent)

ATP.1: 15 residues within 4Å: Chain B: D.134, V.135, A.136, P.175, G.176, T.177, G.178, K.179, S.180, Y.181, Q.233, M.307, I.310, G.336, S.337 12 PLIP interactions: 12 interactions with chain B Hydrogen bonds: B:A.136, B:A.136, B:G.176, B:T.177, B:G.178, B:K.179, B:S.180, B:S.180, B:Y.181, B:Q.233 Salt bridges: B:K.179 pi-Stacking: B:Y.181 ATP.2: 15 residues within 4Å: Chain B: L.257, N.261, R.289 Chain C: D.134, P.175, G.176, T.177, G.178, K.179, S.180, Y.181, N.277, M.307, G.336, S.337 15 PLIP interactions: 11 interactions with chain C, 4 interactions with chain B Hydrogen bonds: C:G.176, C:G.178, C:K.179, C:S.180, C:S.180, C:Y.181, C:N.277, C:N.277, B:N.261 Salt bridges: C:K.179, B:R.289, B:R.289, B:R.289 pi-Stacking: C:Y.181, C:Y.181 ATP.3: 17 residues within 4Å: Chain C: N.261, N.265, R.289 Chain D: V.135, A.136, P.175, G.176, T.177, G.178, K.179, S.180, Y.181, Q.233, N.277, M.307, G.336, S.337 19 PLIP interactions: 15 interactions with chain D, 4 interactions with chain C Hydrogen bonds: D:A.136, D:A.136, D:G.176, D:T.177, D:G.178, D:K.179, D:S.180, D:S.180, D:Y.181, D:D.232, D:Q.233, D:N.277, D:N.277, C:N.261, C:N.265, C:R.289 Salt bridges: D:K.179, D:K.179, C:R.289 ATP.4: 19 residues within 4Å: Chain D: N.261, N.265, R.289 Chain E: D.134, V.135, A.136, P.174, P.175, G.176, T.177, G.178, K.179, S.180, Y.181, Q.233, N.277, M.307, G.336, S.337 19 PLIP interactions: 4 interactions with chain D, 15 interactions with chain E Hydrogen bonds: D:N.261, D:N.265, D:R.289, E:A.136, E:A.136, E:P.174, E:G.176, E:T.177, E:G.178, E:K.179, E:S.180, E:S.180, E:Y.181, E:Q.233, E:N.277, E:N.277 Salt bridges: D:R.289, E:K.179, E:K.179 ATP.5: 17 residues within 4Å: Chain E: V.263, N.265, R.289 Chain F: A.136, P.175, G.176, T.177, G.178, K.179, S.180, Y.181, D.232, Q.233, N.277, M.307, G.336, S.337 18 PLIP interactions: 15 interactions with chain F, 3 interactions with chain E Hydrogen bonds: F:A.136, F:A.136, F:G.176, F:T.177, F:G.178, F:K.179, F:S.180, F:S.180, F:S.180, F:Y.181, F:D.232, F:Q.233, F:N.277, E:N.265 Salt bridges: F:K.179, E:R.289, E:R.289 pi-Stacking: F:Y.181

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Sun, S. et al., Cryo-EM structures of the ATP-bound Vps4(E233Q) hexamer and its complex with Vta1 at near-atomic resolution. Nat Commun (2017)

Release Date

2017-08-09

Peptides

Vacuolar protein sorting-associated protein 4: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

Vacuolar protein sorting-associated protein 4

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