SMTL ID : 7rlg.1

Cryo-EM structure of human p97-D592N mutant bound to ADP.

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-hexamer

Ligands

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

ADP.1: 15 residues within 4Å: Chain A: D.220, I.221, G.222, P.262, G.263, T.264, G.265, K.266, T.267, L.268, I.395, H.399, G.423, A.424 Chain F: R.374 10 PLIP interactions: 2 interactions with chain F, 8 interactions with chain A Salt bridges: F:R.374, F:R.374, A:K.266 Hydrogen bonds: A:G.222, A:G.263, A:T.264, A:T.264, A:G.265, A:K.266, A:T.267 ADP.2: 12 residues within 4Å: Chain A: D.493, G.495, P.535, G.536, C.537, G.538, K.539, T.540, L.541, I.671, N.675, T.703 11 PLIP interactions: 11 interactions with chain A Hydrogen bonds: A:G.495, A:G.536, A:C.537, A:C.537, A:G.538, A:K.539, A:T.540, A:T.540, A:N.675, A:T.703 Salt bridges: A:K.539 ADP.3: 15 residues within 4Å: Chain A: R.374 Chain B: D.220, I.221, G.222, P.262, G.263, T.264, G.265, K.266, T.267, L.268, I.395, H.399, G.423, A.424 10 PLIP interactions: 8 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:G.222, B:G.263, B:T.264, B:T.264, B:G.265, B:K.266, B:T.267 Salt bridges: B:K.266, A:R.374, A:R.374 ADP.4: 12 residues within 4Å: Chain B: D.493, G.495, P.535, G.536, C.537, G.538, K.539, T.540, L.541, I.671, N.675, T.703 11 PLIP interactions: 11 interactions with chain B Hydrogen bonds: B:G.495, B:G.536, B:C.537, B:C.537, B:G.538, B:K.539, B:T.540, B:T.540, B:N.675, B:T.703 Salt bridges: B:K.539 ADP.5: 15 residues within 4Å: Chain B: R.374 Chain C: D.220, I.221, G.222, P.262, G.263, T.264, G.265, K.266, T.267, L.268, I.395, H.399, G.423, A.424 9 PLIP interactions: 8 interactions with chain C, 1 interactions with chain B Hydrogen bonds: C:G.222, C:G.263, C:T.264, C:T.264, C:G.265, C:K.266, C:T.267 Salt bridges: C:K.266, B:R.374 ADP.6: 12 residues within 4Å: Chain C: D.493, G.495, P.535, G.536, C.537, G.538, K.539, T.540, L.541, I.671, N.675, T.703 11 PLIP interactions: 11 interactions with chain C Hydrogen bonds: C:G.495, C:G.536, C:C.537, C:C.537, C:G.538, C:K.539, C:T.540, C:T.540, C:N.675, C:T.703 Salt bridges: C:K.539 ADP.7: 15 residues within 4Å: Chain C: R.374 Chain D: D.220, I.221, G.222, P.262, G.263, T.264, G.265, K.266, T.267, L.268, I.395, H.399, G.423, A.424 10 PLIP interactions: 8 interactions with chain D, 2 interactions with chain C Hydrogen bonds: D:G.222, D:G.263, D:T.264, D:T.264, D:G.265, D:K.266, D:T.267 Salt bridges: D:K.266, C:R.374, C:R.374 ADP.8: 12 residues within 4Å: Chain D: D.493, G.495, P.535, G.536, C.537, G.538, K.539, T.540, L.541, I.671, N.675, T.703 11 PLIP interactions: 11 interactions with chain D Hydrogen bonds: D:G.495, D:G.536, D:C.537, D:C.537, D:G.538, D:K.539, D:T.540, D:T.540, D:N.675, D:T.703 Salt bridges: D:K.539 ADP.9: 15 residues within 4Å: Chain D: R.374 Chain E: D.220, I.221, G.222, P.262, G.263, T.264, G.265, K.266, T.267, L.268, I.395, H.399, G.423, A.424 10 PLIP interactions: 8 interactions with chain E, 2 interactions with chain D Hydrogen bonds: E:G.222, E:G.263, E:T.264, E:T.264, E:G.265, E:K.266, E:T.267 Salt bridges: E:K.266, D:R.374, D:R.374 ADP.10: 12 residues within 4Å: Chain E: D.493, G.495, P.535, G.536, C.537, G.538, K.539, T.540, L.541, I.671, N.675, T.703 11 PLIP interactions: 11 interactions with chain E Hydrogen bonds: E:G.495, E:G.536, E:C.537, E:C.537, E:G.538, E:K.539, E:T.540, E:T.540, E:N.675, E:T.703 Salt bridges: E:K.539 ADP.11: 15 residues within 4Å: Chain E: R.374 Chain F: D.220, I.221, G.222, P.262, G.263, T.264, G.265, K.266, T.267, L.268, I.395, H.399, G.423, A.424 10 PLIP interactions: 8 interactions with chain F, 2 interactions with chain E Hydrogen bonds: F:G.222, F:G.263, F:T.264, F:T.264, F:G.265, F:K.266, F:T.267 Salt bridges: F:K.266, E:R.374, E:R.374 ADP.12: 12 residues within 4Å: Chain F: D.493, G.495, P.535, G.536, C.537, G.538, K.539, T.540, L.541, I.671, N.675, T.703 11 PLIP interactions: 11 interactions with chain F Hydrogen bonds: F:G.495, F:G.536, F:C.537, F:C.537, F:G.538, F:K.539, F:T.540, F:T.540, F:N.675, F:T.703 Salt bridges: F:K.539

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Caffrey, B. et al., AAA+ ATPase p97/VCP mutants and inhibitor binding disrupt inter-domain coupling and subsequent allosteric activation. J.Biol.Chem. (2021)

Release Date

2021-09-22

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