SMTL ID : 7rlc.1

Cryo-EM structure of human p97-A232E 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: 17 residues within 4Å: Chain A: D.220, G.222, P.262, G.263, T.264, G.265, K.266, T.267, L.268, N.363, I.395, I.398, H.399, G.423, A.424 Chain F: R.374 Ligands: MG.3 9 PLIP interactions: 9 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:L.268 Salt bridges: A:K.266, A:K.266 AGS.2: 16 residues within 4Å: Chain A: D.493, G.495, G.536, C.537, G.538, K.539, T.540, L.541, N.639, I.671, N.675, T.703 Chain F: R.650, P.651, R.781 Ligands: MG.4 13 PLIP interactions: 12 interactions with chain A, 1 interactions with chain F 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:T.540, A:N.639, A:N.675, F:R.781 Salt bridges: A:K.539 AGS.5: 17 residues within 4Å: Chain A: R.374 Chain B: D.220, G.222, P.262, G.263, T.264, G.265, K.266, T.267, L.268, N.363, I.395, I.398, H.399, G.423, A.424 Ligands: MG.7 9 PLIP interactions: 9 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:L.268 Salt bridges: B:K.266, B:K.266 AGS.6: 16 residues within 4Å: Chain A: R.650, P.651, R.781 Chain B: D.493, G.495, G.536, C.537, G.538, K.539, T.540, L.541, N.639, I.671, N.675, T.703 Ligands: MG.8 12 PLIP interactions: 1 interactions with chain A, 11 interactions with chain B Hydrogen bonds: A:R.781, 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:N.639, B:N.675 Salt bridges: B:K.539 AGS.9: 17 residues within 4Å: Chain B: R.374 Chain C: D.220, G.222, P.262, G.263, T.264, G.265, K.266, T.267, L.268, N.363, I.395, I.398, H.399, G.423, A.424 Ligands: MG.11 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:L.268 Salt bridges: C:K.266, C:K.266 AGS.10: 15 residues within 4Å: Chain B: P.651, R.781 Chain C: D.493, G.495, G.536, C.537, G.538, K.539, T.540, L.541, N.639, I.671, N.675, T.703 Ligands: MG.12 13 PLIP interactions: 12 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:T.540, C:N.639, C:N.675, B:R.781 Salt bridges: C:K.539 AGS.13: 17 residues within 4Å: Chain C: R.374 Chain D: D.220, G.222, P.262, G.263, T.264, G.265, K.266, T.267, L.268, N.363, I.395, I.398, H.399, G.423, A.424 Ligands: MG.15 9 PLIP interactions: 9 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:L.268 Salt bridges: D:K.266, D:K.266 AGS.14: 16 residues within 4Å: Chain C: R.650, P.651, R.781 Chain D: D.493, G.495, G.536, C.537, G.538, K.539, T.540, L.541, N.639, I.671, N.675, T.703 Ligands: MG.16 14 PLIP interactions: 12 interactions with chain D, 2 interactions with chain C 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:T.540, D:N.639, D:N.675, C:R.650, C:R.781 Salt bridges: D:K.539 AGS.17: 16 residues within 4Å: Chain E: D.220, G.222, P.262, G.263, T.264, G.265, K.266, T.267, L.268, N.363, I.395, I.398, H.399, G.423, A.424 Ligands: MG.19 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:L.268 Salt bridges: E:K.266, E:K.266 AGS.18: 15 residues within 4Å: Chain D: P.651, R.781 Chain E: D.493, G.495, G.536, C.537, G.538, K.539, T.540, L.541, N.639, I.671, N.675, T.703 Ligands: MG.20 13 PLIP interactions: 12 interactions with chain E, 1 interactions with chain D Hydrogen bonds: 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:T.540, E:N.639, E:N.675, D:R.781 Salt bridges: E:K.539 AGS.21: 16 residues within 4Å: Chain F: D.220, G.222, P.262, G.263, T.264, G.265, K.266, T.267, L.268, N.363, I.395, I.398, H.399, G.423, A.424 Ligands: MG.23 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:L.268 Salt bridges: F:K.266, F:K.266 AGS.22: 16 residues within 4Å: Chain E: R.650, P.651, R.781 Chain F: D.493, G.495, G.536, C.537, G.538, K.539, T.540, L.541, N.639, I.671, N.675, T.703 Ligands: MG.24 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:N.639, 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.267, D.319 Ligands: AGS.1 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:T.267 MG.4: 2 residues within 4Å: Chain A: T.540 Ligands: AGS.2 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:T.540 MG.7: 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.8: 2 residues within 4Å: Chain B: T.540 Ligands: AGS.6 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:T.540 MG.11: 2 residues within 4Å: Chain C: T.267 Ligands: AGS.9 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:T.267 MG.12: 2 residues within 4Å: Chain C: T.540 Ligands: AGS.10 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:T.540 MG.15: 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.16: 2 residues within 4Å: Chain D: T.540 Ligands: AGS.14 1 PLIP interactions: 1 interactions with chain D Metal complexes: D:T.540 MG.19: 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.20: 2 residues within 4Å: Chain E: T.540 Ligands: AGS.18 1 PLIP interactions: 1 interactions with chain E Metal complexes: E:T.540 MG.23: 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 MG.24: 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

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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