SMTL ID : 7rla.1

Cryo-EM structure of human p97-R191Q 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: 16 residues within 4Å: Chain A: D.220, I.221, G.222, G.263, T.264, G.265, K.266, T.267, L.268, I.395, H.399, G.423, A.424 Chain F: R.374, F.375 Ligands: MG.4 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:G.222, A:G.222, A:G.263, A:G.265, A:K.266, A:T.267, A:T.267, A:T.267, A:L.268 Salt bridges: A:K.266 AGS.2: 17 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, I.671, N.675, A.700, T.703 Chain F: P.651, R.781 Ligands: MG.3 11 PLIP interactions: 11 interactions with chain A Hydrogen bonds: A:G.495, A:G.495, A:G.536, A:C.537, A:G.538, A:K.539, A:T.540, A:T.540, A:L.541, A:N.675 Salt bridges: A:K.539 AGS.5: 15 residues within 4Å: Chain A: F.375 Chain B: D.220, I.221, G.222, G.263, T.264, G.265, K.266, T.267, L.268, I.395, H.399, G.423, A.424 Ligands: MG.8 10 PLIP interactions: 10 interactions with chain B Hydrogen bonds: B:G.222, B:G.222, B:G.263, B:G.265, B:K.266, B:T.267, B:T.267, B:T.267, B:L.268 Salt bridges: B:K.266 AGS.6: 17 residues within 4Å: Chain A: 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, I.671, N.675, A.700, T.703 Ligands: MG.7 11 PLIP interactions: 11 interactions with chain B Hydrogen bonds: B:G.495, B:G.495, B:G.536, B:C.537, B:G.538, B:K.539, B:T.540, B:T.540, B:L.541, B:N.675 Salt bridges: B:K.539 AGS.9: 15 residues within 4Å: Chain B: F.375 Chain C: D.220, I.221, G.222, G.263, T.264, G.265, K.266, T.267, L.268, I.395, H.399, G.423, A.424 Ligands: MG.12 10 PLIP interactions: 10 interactions with chain C Hydrogen bonds: C:G.222, C:G.222, C:G.263, C:G.265, C:K.266, C:T.267, C:T.267, C:T.267, C:L.268 Salt bridges: C:K.266 AGS.10: 17 residues within 4Å: Chain B: 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, I.671, N.675, A.700, T.703 Ligands: MG.11 12 PLIP interactions: 11 interactions with chain C, 1 interactions with chain B Hydrogen bonds: C:G.495, C:G.495, C:G.536, C:C.537, C:G.538, C:K.539, C:T.540, C:T.540, C:L.541, C:N.675, B:R.781 Salt bridges: C:K.539 AGS.13: 15 residues within 4Å: Chain C: F.375 Chain D: D.220, I.221, G.222, G.263, T.264, G.265, K.266, T.267, L.268, I.395, H.399, G.423, A.424 Ligands: MG.16 10 PLIP interactions: 10 interactions with chain D Hydrogen bonds: D:G.222, D:G.222, D:G.263, D:G.265, D:K.266, D:T.267, D:T.267, D:T.267, D:L.268 Salt bridges: D:K.266 AGS.14: 17 residues within 4Å: Chain C: 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, I.671, N.675, A.700, T.703 Ligands: MG.15 11 PLIP interactions: 11 interactions with chain D Hydrogen bonds: D:G.495, D:G.495, D:G.536, D:C.537, D:G.538, D:K.539, D:T.540, D:T.540, D:L.541, D:N.675 Salt bridges: D:K.539 AGS.17: 15 residues within 4Å: Chain D: F.375 Chain E: D.220, I.221, G.222, G.263, T.264, G.265, K.266, T.267, L.268, I.395, H.399, G.423, A.424 Ligands: MG.20 10 PLIP interactions: 10 interactions with chain E Hydrogen bonds: E:G.222, E:G.222, E:G.263, E:G.265, E:K.266, E:T.267, E:T.267, E:T.267, E:L.268 Salt bridges: E:K.266 AGS.18: 17 residues within 4Å: Chain D: 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, I.671, N.675, A.700, T.703 Ligands: MG.19 12 PLIP interactions: 1 interactions with chain D, 11 interactions with chain E Hydrogen bonds: D:R.781, E:G.495, E:G.495, E:G.536, E:C.537, E:G.538, E:K.539, E:T.540, E:T.540, E:L.541, E:N.675 Salt bridges: E:K.539 AGS.21: 15 residues within 4Å: Chain E: F.375 Chain F: D.220, I.221, G.222, G.263, T.264, G.265, K.266, T.267, L.268, I.395, H.399, G.423, A.424 Ligands: MG.24 10 PLIP interactions: 10 interactions with chain F Hydrogen bonds: F:G.222, F:G.222, F:G.263, F:G.265, F:K.266, F:T.267, F:T.267, F:T.267, F:L.268 Salt bridges: F:K.266 AGS.22: 17 residues within 4Å: Chain E: 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, I.671, N.675, A.700, T.703 Ligands: MG.23 12 PLIP interactions: 11 interactions with chain F, 1 interactions with chain E Hydrogen bonds: F:G.495, F:G.495, F:G.536, F:C.537, F:G.538, F:K.539, F:T.540, F:T.540, F:L.541, F:N.675, E:R.781 Salt bridges: F:K.539

12 x MG: MAGNESIUM ION(Non-covalent)

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

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

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