SMTL ID : 7rl7.1

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

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-hexamer

Ligands

12 x AGS: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER(Non-covalent)

AGS.1: 20 residues within 4Å: Chain A: D.220, I.221, G.222, C.224, P.262, G.263, T.264, G.265, K.266, T.267, L.268, N.363, I.395, H.399, G.423, A.424 Chain F: R.374, F.375, R.377 Ligands: MG.3 11 PLIP interactions: 1 interactions with chain F, 10 interactions with chain A Hydrogen bonds: F:R.377, A:G.222, A:G.263, A:T.264, A:T.264, A:G.265, A:K.266, A:T.267, A:L.268, A:N.363 Salt bridges: A:K.266 AGS.2: 20 residues within 4Å: Chain A: D.493, I.494, G.495, P.535, G.536, C.537, G.538, K.539, T.540, L.541, N.639, I.671, N.675, G.699, A.700, T.703 Chain F: R.650, P.651, R.781 Ligands: MG.4 14 PLIP interactions: 12 interactions with chain A, 2 interactions with chain F 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:L.541, A:N.639, A:N.675, F:R.781, F:R.781 Salt bridges: A:K.539 AGS.5: 19 residues within 4Å: Chain A: R.374, F.375 Chain B: D.220, I.221, G.222, C.224, P.262, G.263, T.264, G.265, K.266, T.267, L.268, N.363, I.395, H.399, G.423, A.424 Ligands: MG.7 11 PLIP interactions: 10 interactions with chain B, 1 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, B:L.268, B:N.363, A:R.377 Salt bridges: B:K.266 AGS.6: 20 residues within 4Å: Chain A: R.650, P.651, R.781 Chain B: D.493, I.494, G.495, P.535, G.536, C.537, G.538, K.539, T.540, L.541, N.639, I.671, N.675, G.699, A.700, T.703 Ligands: MG.8 14 PLIP interactions: 12 interactions with chain B, 2 interactions with chain A 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:L.541, B:N.639, B:N.675, A:R.781, A:R.781 Salt bridges: B:K.539 AGS.9: 19 residues within 4Å: Chain B: R.374, F.375 Chain C: D.220, I.221, G.222, C.224, P.262, G.263, T.264, G.265, K.266, T.267, L.268, N.363, I.395, H.399, G.423, A.424 Ligands: MG.11 11 PLIP interactions: 10 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, C:L.268, C:N.363, B:R.377 Salt bridges: C:K.266 AGS.10: 20 residues within 4Å: Chain B: R.650, P.651, R.781 Chain C: D.493, I.494, G.495, P.535, G.536, C.537, G.538, K.539, T.540, L.541, N.639, I.671, N.675, G.699, A.700, T.703 Ligands: MG.12 14 PLIP interactions: 12 interactions with chain C, 2 interactions with chain B 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:L.541, C:N.639, C:N.675, B:R.781, B:R.781 Salt bridges: C:K.539 AGS.13: 20 residues within 4Å: Chain C: R.374, F.375, R.377 Chain D: D.220, I.221, G.222, C.224, P.262, G.263, T.264, G.265, K.266, T.267, L.268, N.363, I.395, H.399, G.423, A.424 Ligands: MG.15 11 PLIP interactions: 10 interactions with chain D, 1 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, D:L.268, D:N.363, C:R.377 Salt bridges: D:K.266 AGS.14: 20 residues within 4Å: Chain C: R.650, P.651, R.781 Chain D: D.493, I.494, G.495, P.535, G.536, C.537, G.538, K.539, T.540, L.541, N.639, I.671, N.675, G.699, A.700, T.703 Ligands: MG.16 15 PLIP interactions: 13 interactions with chain D, 2 interactions with chain C 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:T.540, D:L.541, D:N.639, D:N.675, C:R.781, C:R.781 Salt bridges: D:K.539 AGS.17: 20 residues within 4Å: Chain D: R.374, F.375, R.377 Chain E: D.220, I.221, G.222, C.224, P.262, G.263, T.264, G.265, K.266, T.267, L.268, N.363, I.395, H.399, G.423, A.424 Ligands: MG.19 11 PLIP interactions: 10 interactions with chain E, 1 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, E:L.268, E:N.363, D:R.377 Salt bridges: E:K.266 AGS.18: 20 residues within 4Å: Chain D: R.650, P.651, R.781 Chain E: D.493, I.494, G.495, P.535, G.536, C.537, G.538, K.539, T.540, L.541, N.639, I.671, N.675, G.699, A.700, T.703 Ligands: MG.20 14 PLIP interactions: 12 interactions with chain E, 2 interactions with chain D 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:L.541, E:N.639, E:N.675, D:R.781, D:R.781 Salt bridges: E:K.539 AGS.21: 20 residues within 4Å: Chain E: R.374, F.375, R.377 Chain F: D.220, I.221, G.222, C.224, P.262, G.263, T.264, G.265, K.266, T.267, L.268, N.363, I.395, H.399, G.423, A.424 Ligands: MG.23 11 PLIP interactions: 10 interactions with chain F, 1 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, F:L.268, F:N.363, E:R.377 Salt bridges: F:K.266 AGS.22: 20 residues within 4Å: Chain E: R.650, P.651, R.781 Chain F: D.493, I.494, G.495, P.535, G.536, C.537, G.538, K.539, T.540, L.541, N.639, I.671, N.675, G.699, A.700, T.703 Ligands: MG.24 14 PLIP interactions: 12 interactions with chain F, 2 interactions with chain E 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:L.541, F:N.639, F:N.675, E:R.781, E:R.781 Salt bridges: F:K.539

12 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 3 residues within 4Å: Chain A: T.267, D.319 Ligands: AGS.1 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:T.267, A:D.319, A:D.319 MG.4: 3 residues within 4Å: Chain A: T.540, D.592 Ligands: AGS.2 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:T.540, A:D.592 MG.7: 3 residues within 4Å: Chain B: T.267, D.319 Ligands: AGS.5 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:T.267, B:D.319, B:D.319 MG.8: 3 residues within 4Å: Chain B: T.540, D.592 Ligands: AGS.6 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:T.540, B:D.592 MG.11: 3 residues within 4Å: Chain C: T.267, D.319 Ligands: AGS.9 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:T.267, C:D.319, C:D.319 MG.12: 3 residues within 4Å: Chain C: T.540, D.592 Ligands: AGS.10 2 PLIP interactions: 2 interactions with chain C Metal complexes: C:T.540, C:D.592 MG.15: 3 residues within 4Å: Chain D: T.267, D.319 Ligands: AGS.13 3 PLIP interactions: 3 interactions with chain D Metal complexes: D:T.267, D:D.319, D:D.319 MG.16: 3 residues within 4Å: Chain D: T.540, D.592 Ligands: AGS.14 2 PLIP interactions: 2 interactions with chain D Metal complexes: D:T.540, D:D.592 MG.19: 3 residues within 4Å: Chain E: T.267, D.319 Ligands: AGS.17 3 PLIP interactions: 3 interactions with chain E Metal complexes: E:T.267, E:D.319, E:D.319 MG.20: 3 residues within 4Å: Chain E: T.540, D.592 Ligands: AGS.18 2 PLIP interactions: 2 interactions with chain E Metal complexes: E:T.540, E:D.592 MG.23: 3 residues within 4Å: Chain F: T.267, D.319 Ligands: AGS.21 3 PLIP interactions: 3 interactions with chain F Metal complexes: F:T.267, F:D.319, F:D.319 MG.24: 3 residues within 4Å: Chain F: T.540, D.592 Ligands: AGS.22 2 PLIP interactions: 2 interactions with chain F Metal complexes: F:T.540, F:D.592

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