SMTL ID : 7rl6.1

Cryo-EM structure of human p97-R155H mutant bound to ADP.

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-hexamer

Ligands

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

ADP.1: 14 residues within 4Å: Chain A: D.222, I.223, G.224, P.264, G.265, T.266, G.267, K.268, T.269, L.270, I.397, H.401, G.425, A.426 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:G.224, A:G.265, A:T.266, A:G.267, A:K.268, A:T.269, A:T.269, A:T.269, A:L.270 Salt bridges: A:K.268 ADP.2: 14 residues within 4Å: Chain A: D.495, I.496, G.497, P.537, G.538, C.539, G.540, K.541, T.542, L.543, I.673, G.701, A.702, T.705 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:G.497, A:G.538, A:C.539, A:G.540, A:K.541, A:T.542, A:T.542, A:T.542, A:L.543 Salt bridges: A:K.541 ADP.3: 14 residues within 4Å: Chain B: D.222, I.223, G.224, P.264, G.265, T.266, G.267, K.268, T.269, L.270, I.397, H.401, G.425, A.426 10 PLIP interactions: 10 interactions with chain B Hydrogen bonds: B:G.224, B:G.265, B:T.266, B:G.267, B:K.268, B:T.269, B:T.269, B:T.269, B:L.270 Salt bridges: B:K.268 ADP.4: 13 residues within 4Å: Chain B: D.495, I.496, G.497, P.537, G.538, C.539, G.540, K.541, T.542, L.543, I.673, G.701, T.705 11 PLIP interactions: 11 interactions with chain B Hydrogen bonds: B:G.497, B:G.497, B:G.538, B:C.539, B:G.540, B:K.541, B:T.542, B:T.542, B:T.542, B:L.543 Salt bridges: B:K.541 ADP.5: 14 residues within 4Å: Chain C: D.222, I.223, G.224, P.264, G.265, T.266, G.267, K.268, T.269, L.270, I.397, H.401, G.425, A.426 10 PLIP interactions: 10 interactions with chain C Hydrogen bonds: C:G.224, C:G.265, C:T.266, C:G.267, C:K.268, C:T.269, C:T.269, C:T.269, C:L.270 Salt bridges: C:K.268 ADP.6: 14 residues within 4Å: Chain C: D.495, I.496, G.497, P.537, G.538, C.539, G.540, K.541, T.542, L.543, I.673, G.701, A.702, T.705 12 PLIP interactions: 12 interactions with chain C Hydrogen bonds: C:G.497, C:G.497, C:G.538, C:C.539, C:G.540, C:K.541, C:T.542, C:T.542, C:T.542, C:L.543, C:N.677 Salt bridges: C:K.541 ADP.7: 14 residues within 4Å: Chain D: D.222, I.223, G.224, P.264, G.265, T.266, G.267, K.268, T.269, L.270, I.397, H.401, G.425, A.426 10 PLIP interactions: 10 interactions with chain D Hydrogen bonds: D:G.224, D:G.224, D:G.265, D:G.267, D:K.268, D:T.269, D:T.269, D:T.269, D:L.270 Salt bridges: D:K.268 ADP.8: 14 residues within 4Å: Chain D: D.495, I.496, G.497, L.499, P.537, G.538, C.539, G.540, K.541, T.542, L.543, I.673, G.701, T.705 9 PLIP interactions: 9 interactions with chain D Hydrogen bonds: D:G.497, D:G.497, D:G.538, D:C.539, D:G.540, D:K.541, D:T.542, D:T.542, D:L.543 ADP.9: 14 residues within 4Å: Chain E: D.222, I.223, G.224, P.264, G.265, T.266, G.267, K.268, T.269, L.270, I.397, H.401, G.425, A.426 10 PLIP interactions: 10 interactions with chain E Hydrogen bonds: E:G.224, E:G.265, E:T.266, E:G.267, E:K.268, E:T.269, E:T.269, E:T.269, E:L.270 Salt bridges: E:K.268 ADP.10: 14 residues within 4Å: Chain E: D.495, I.496, G.497, P.537, G.538, C.539, G.540, K.541, T.542, L.543, I.673, G.701, A.702, T.705 12 PLIP interactions: 12 interactions with chain E Hydrogen bonds: E:G.497, E:G.497, E:G.538, E:C.539, E:G.540, E:K.541, E:T.542, E:T.542, E:T.542, E:L.543, E:N.677 Salt bridges: E:K.541 ADP.11: 14 residues within 4Å: Chain F: D.222, I.223, G.224, P.264, G.265, T.266, G.267, K.268, T.269, L.270, I.397, H.401, G.425, A.426 10 PLIP interactions: 10 interactions with chain F Hydrogen bonds: F:G.224, F:G.265, F:T.266, F:G.267, F:K.268, F:T.269, F:T.269, F:T.269, F:L.270 Salt bridges: F:K.268 ADP.12: 14 residues within 4Å: Chain F: D.495, I.496, G.497, P.537, G.538, C.539, G.540, K.541, T.542, L.543, I.673, N.677, G.701, T.705 11 PLIP interactions: 11 interactions with chain F Hydrogen bonds: F:G.497, F:G.497, F:G.538, F:C.539, F:G.540, F:K.541, F:T.542, F:T.542, F:T.542, F:L.543, F:N.677

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