SMTL ID : 7bpa.1

Human AAA+ ATPase VCP mutant - T76A, AMP-PNP-bound form, Conformation I

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY 3.30 Å

Oligo State

homo-hexamer

Ligands

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

ADP.1: 14 residues within 4Å: Chain A: D.205, I.206, G.207, G.248, T.249, G.250, T.252, L.253, R.256, I.380, H.384, G.408, A.409 Chain B: K.336 6 PLIP interactions: 5 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:G.207, A:G.207, A:G.250, A:T.252 Salt bridges: A:R.256, B:K.336 ADP.4: 14 residues within 4Å: Chain B: D.205, I.206, G.207, G.248, T.249, G.250, T.252, L.253, R.256, I.380, H.384, G.408, A.409 Chain C: K.336 5 PLIP interactions: 4 interactions with chain B, 1 interactions with chain C Hydrogen bonds: B:G.207, B:G.207, B:G.250, B:R.256 Salt bridges: C:K.336 ADP.6: 14 residues within 4Å: Chain C: D.205, I.206, G.207, G.248, T.249, G.250, T.252, L.253, R.256, I.380, H.384, G.408, A.409 Chain D: K.336 6 PLIP interactions: 5 interactions with chain C, 1 interactions with chain D Hydrogen bonds: C:G.207, C:G.207, C:G.250, C:R.256, C:G.408 Salt bridges: D:K.336 ADP.8: 14 residues within 4Å: Chain D: D.205, I.206, G.207, G.248, T.249, G.250, T.252, L.253, R.256, I.380, H.384, G.408, A.409 Chain E: K.336 6 PLIP interactions: 1 interactions with chain E, 5 interactions with chain D Salt bridges: E:K.336, D:R.256 Hydrogen bonds: D:G.207, D:G.207, D:G.250, D:T.252 ADP.10: 14 residues within 4Å: Chain E: D.205, I.206, G.207, G.248, T.249, G.250, T.252, L.253, R.256, I.380, H.384, G.408, A.409 Chain F: K.336 5 PLIP interactions: 4 interactions with chain E, 1 interactions with chain F Hydrogen bonds: E:G.207, E:G.207, E:G.250, E:R.256 Salt bridges: F:K.336 ADP.12: 14 residues within 4Å: Chain A: K.336 Chain F: D.205, I.206, G.207, G.248, T.249, G.250, T.252, L.253, R.256, I.380, H.384, G.408, A.409 6 PLIP interactions: 5 interactions with chain F, 1 interactions with chain A Hydrogen bonds: F:G.207, F:G.207, F:G.250, F:R.256, F:G.408 Salt bridges: A:K.336

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

ANP.2: 14 residues within 4Å: Chain A: R.635 Chain F: D.478, I.479, G.480, P.520, G.521, C.522, G.523, K.524, T.525, L.526, I.656, G.684, A.685 8 PLIP interactions: 8 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 ANP.3: 14 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, G.684, A.685 Chain B: R.635 7 PLIP interactions: 7 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 ANP.5: 14 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, G.684, A.685 Chain C: R.635 8 PLIP interactions: 8 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 ANP.7: 14 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, G.684, A.685 Chain D: R.635 8 PLIP interactions: 8 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 ANP.9: 14 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, G.684, A.685 Chain E: R.635 8 PLIP interactions: 8 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 ANP.11: 14 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, G.684, A.685 Chain F: R.635 8 PLIP interactions: 8 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

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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