SMTL ID : 7bp9.1

Human AAA+ ATPase VCP mutant - T76E, ADP-bound form

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY 3.60 Å

Oligo State

homo-hexamer

Ligands

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

ADP.1: 15 residues within 4Å: Chain A: D.205, I.206, G.207, G.248, T.249, G.250, K.251, T.252, L.253, I.380, H.384, G.408, A.409 Chain B: K.236, R.359 12 PLIP interactions: 10 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:G.207, A:G.248, A:T.249, A:T.249, A:G.250, A:K.251, A:T.252, A:T.252, A:L.253, B:K.236 Salt bridges: A:K.251, B:R.359 ADP.2: 15 residues within 4Å: Chain A: D.478, I.479, G.480, P.520, G.521, C.522, G.523, K.524, T.525, L.526, I.656, N.660, G.684, A.685, T.688 12 PLIP interactions: 12 interactions with chain A Hydrogen bonds: A:G.480, A:G.480, A:G.521, A:C.522, A:G.523, A:K.524, A:T.525, A:T.525, A:T.525, A:L.526, A:T.688 Salt bridges: A:K.524 ADP.3: 14 residues within 4Å: Chain B: D.205, I.206, G.207, G.248, T.249, G.250, K.251, T.252, L.253, I.380, H.384, G.408, A.409 Chain C: R.359 11 PLIP interactions: 10 interactions with chain B, 1 interactions with chain C Hydrogen bonds: B:G.207, B:G.248, B:T.249, B:T.249, B:G.250, B:K.251, B:T.252, B:T.252, B:L.253 Salt bridges: B:K.251, C:R.359 ADP.4: 15 residues within 4Å: Chain B: D.478, I.479, G.480, P.520, G.521, C.522, G.523, K.524, T.525, L.526, I.656, N.660, G.684, A.685, T.688 12 PLIP interactions: 12 interactions with chain B Hydrogen bonds: B:G.480, B:G.480, B:G.521, B:C.522, B:G.523, B:K.524, B:T.525, B:T.525, B:T.525, B:L.526, B:T.688 Salt bridges: B:K.524 ADP.5: 14 residues within 4Å: Chain C: D.205, I.206, G.207, G.248, T.249, G.250, K.251, T.252, L.253, I.380, H.384, G.408, A.409 Chain D: R.359 11 PLIP interactions: 1 interactions with chain D, 10 interactions with chain C Salt bridges: D:R.359, C:K.251 Hydrogen bonds: C:G.207, C:G.248, C:T.249, C:T.249, C:G.250, C:K.251, C:T.252, C:T.252, C:L.253 ADP.6: 15 residues within 4Å: Chain C: D.478, I.479, G.480, P.520, G.521, C.522, G.523, K.524, T.525, L.526, I.656, N.660, G.684, A.685, T.688 12 PLIP interactions: 12 interactions with chain C Hydrogen bonds: C:G.480, C:G.480, C:G.521, C:C.522, C:G.523, C:K.524, C:T.525, C:T.525, C:T.525, C:L.526, C:T.688 Salt bridges: C:K.524 ADP.7: 14 residues within 4Å: Chain D: D.205, I.206, G.207, G.248, T.249, G.250, K.251, T.252, L.253, I.380, H.384, G.408, A.409 Chain E: R.359 11 PLIP interactions: 10 interactions with chain D, 1 interactions with chain E Hydrogen bonds: D:G.207, D:G.248, D:T.249, D:T.249, D:G.250, D:K.251, D:T.252, D:T.252, D:L.253 Salt bridges: D:K.251, E:R.359 ADP.8: 15 residues within 4Å: Chain D: D.478, I.479, G.480, P.520, G.521, C.522, G.523, K.524, T.525, L.526, I.656, N.660, G.684, A.685, T.688 12 PLIP interactions: 12 interactions with chain D Hydrogen bonds: D:G.480, D:G.480, D:G.521, D:C.522, D:G.523, D:K.524, D:T.525, D:T.525, D:T.525, D:L.526, D:T.688 Salt bridges: D:K.524 ADP.9: 14 residues within 4Å: Chain E: D.205, I.206, G.207, G.248, T.249, G.250, K.251, T.252, L.253, I.380, H.384, G.408, A.409 Chain F: R.359 11 PLIP interactions: 10 interactions with chain E, 1 interactions with chain F Hydrogen bonds: E:G.207, E:G.248, E:T.249, E:T.249, E:G.250, E:K.251, E:T.252, E:T.252, E:L.253 Salt bridges: E:K.251, F:R.359 ADP.10: 15 residues within 4Å: Chain E: D.478, I.479, G.480, P.520, G.521, C.522, G.523, K.524, T.525, L.526, I.656, N.660, G.684, A.685, T.688 12 PLIP interactions: 12 interactions with chain E Hydrogen bonds: E:G.480, E:G.480, E:G.521, E:C.522, E:G.523, E:K.524, E:T.525, E:T.525, E:T.525, E:L.526, E:T.688 Salt bridges: E:K.524 ADP.11: 14 residues within 4Å: Chain A: R.359 Chain F: D.205, I.206, G.207, G.248, T.249, G.250, K.251, T.252, L.253, I.380, H.384, G.408, A.409 11 PLIP interactions: 10 interactions with chain F, 1 interactions with chain A Hydrogen bonds: F:G.207, F:G.248, F:T.249, F:T.249, F:G.250, F:K.251, F:T.252, F:T.252, F:L.253 Salt bridges: F:K.251, A:R.359 ADP.12: 15 residues within 4Å: Chain F: D.478, I.479, G.480, P.520, G.521, C.522, G.523, K.524, T.525, L.526, I.656, N.660, G.684, A.685, T.688 12 PLIP interactions: 12 interactions with chain F Hydrogen bonds: F:G.480, F:G.480, F:G.521, F:C.522, F:G.523, F:K.524, F:T.525, F:T.525, F:T.525, F:L.526, F:T.688 Salt bridges: F:K.524

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zhu, K. et al., The phosphorylation and dephosphorylation switch of VCP/p97 regulates the architecture of centrosome and spindle. Cell Death Differ. (2022)

Release Date

2021-03-31

Peptides

Transitional endoplasmic reticulum ATPase: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

Transitional endoplasmic reticulum ATPase

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