SMTL ID : 7bpb.1

Human AAA+ ATPase VCP mutant - T76E, AMP-PNP bound form, Conformation I

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY 4.30 Å

Oligo State

homo-hexamer

Ligands

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

ADP.1: 10 residues within 4Å: Chain A: D.205, G.248, T.249, G.250, K.251, T.252, L.253, I.380, G.408, A.409 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:G.207, A:G.248, A:G.250, A:T.252, A:L.253 Salt bridges: A:K.251 ADP.4: 10 residues within 4Å: Chain B: D.205, G.248, T.249, G.250, K.251, T.252, L.253, I.380, G.408, A.409 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:G.207, B:G.248, B:G.250, B:T.252, B:L.253 Salt bridges: B:K.251 ADP.6: 10 residues within 4Å: Chain C: D.205, G.248, T.249, G.250, K.251, T.252, L.253, I.380, G.408, A.409 6 PLIP interactions: 6 interactions with chain C Hydrogen bonds: C:G.207, C:G.248, C:G.250, C:T.252, C:L.253 Salt bridges: C:K.251 ADP.8: 10 residues within 4Å: Chain D: D.205, G.248, T.249, G.250, K.251, T.252, L.253, I.380, G.408, A.409 6 PLIP interactions: 6 interactions with chain D Hydrogen bonds: D:G.207, D:G.248, D:G.250, D:T.252, D:L.253 Salt bridges: D:K.251 ADP.10: 10 residues within 4Å: Chain E: D.205, G.248, T.249, G.250, K.251, T.252, L.253, I.380, G.408, A.409 6 PLIP interactions: 6 interactions with chain E Hydrogen bonds: E:G.207, E:G.248, E:G.250, E:T.252, E:L.253 Salt bridges: E:K.251 ADP.12: 10 residues within 4Å: Chain F: D.205, G.248, T.249, G.250, K.251, T.252, L.253, I.380, G.408, A.409 6 PLIP interactions: 6 interactions with chain F Hydrogen bonds: F:G.207, F:G.248, F:G.250, F:T.252, F:L.253 Salt bridges: F:K.251

6 x ANP: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER(Covalent)

ANP.2: 13 residues within 4Å: Chain A: R.635, R.766 Chain F: I.479, P.520, G.521, C.522, G.523, K.524, T.525, L.526, I.656, N.660, G.684 6 PLIP interactions: 2 interactions with chain A, 4 interactions with chain F Hydrogen bonds: A:R.635, A:R.766, F:C.522, F:G.523, F:K.524, F:N.660 ANP.3: 13 residues within 4Å: Chain A: I.479, P.520, G.521, C.522, G.523, K.524, T.525, L.526, I.656, N.660, G.684 Chain B: R.635, R.766 5 PLIP interactions: 4 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:C.522, A:G.523, A:K.524, A:N.660, B:R.635 ANP.5: 13 residues within 4Å: Chain B: I.479, P.520, G.521, C.522, G.523, K.524, T.525, L.526, I.656, N.660, G.684 Chain C: R.635, R.766 6 PLIP interactions: 2 interactions with chain C, 4 interactions with chain B Hydrogen bonds: C:R.635, C:R.766, B:C.522, B:G.523, B:K.524, B:N.660 ANP.7: 13 residues within 4Å: Chain C: I.479, P.520, G.521, C.522, G.523, K.524, T.525, L.526, I.656, N.660, G.684 Chain D: R.635, R.766 6 PLIP interactions: 2 interactions with chain D, 4 interactions with chain C Hydrogen bonds: D:R.635, D:R.766, C:C.522, C:G.523, C:K.524, C:N.660 ANP.9: 13 residues within 4Å: Chain D: I.479, P.520, G.521, C.522, G.523, K.524, T.525, L.526, I.656, N.660, G.684 Chain E: R.635, R.766 6 PLIP interactions: 4 interactions with chain D, 2 interactions with chain E Hydrogen bonds: D:C.522, D:G.523, D:K.524, D:N.660, E:R.635, E:R.766 ANP.11: 13 residues within 4Å: Chain E: I.479, P.520, G.521, C.522, G.523, K.524, T.525, L.526, I.656, N.660, G.684 Chain F: R.635, R.766 5 PLIP interactions: 1 interactions with chain F, 4 interactions with chain E Hydrogen bonds: F:R.635, E:C.522, E:G.523, E:K.524, E:N.660

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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