SMTL ID : 7rlh.1

Cryo-EM structure of human p97-D592N 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.205, I.206, G.207, P.247, G.248, T.249, G.250, K.251, T.252, L.253, N.348, I.380, H.384, G.408, A.409 Ligands: MG.3 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:G.207, A:G.248, A:T.249, A:T.249, A:G.250, A:K.251, A:T.252, A:L.253 Salt bridges: A:K.251 AGS.2: 20 residues within 4Å: Chain A: D.478, I.479, G.480, P.520, G.521, C.522, G.523, K.524, T.525, L.526, N.624, I.656, N.660, G.684, A.685, T.688 Chain F: R.635, P.636, R.766 Ligands: MG.4 14 PLIP interactions: 12 interactions with chain A, 2 interactions with chain F Hydrogen bonds: A:G.480, A:G.521, A:C.522, A:C.522, A:G.523, A:K.524, A:T.525, A:T.525, A:L.526, A:N.624, A:N.660, F:R.766, F:R.766 Salt bridges: A:K.524 AGS.5: 16 residues within 4Å: Chain B: D.205, I.206, G.207, P.247, G.248, T.249, G.250, K.251, T.252, L.253, N.348, I.380, H.384, G.408, A.409 Ligands: MG.7 9 PLIP interactions: 9 interactions with chain B Hydrogen bonds: B:G.207, B:G.248, B:T.249, B:T.249, B:G.250, B:K.251, B:T.252, B:L.253 Salt bridges: B:K.251 AGS.6: 20 residues within 4Å: Chain A: R.635, P.636, R.766 Chain B: D.478, I.479, G.480, P.520, G.521, C.522, G.523, K.524, T.525, L.526, N.624, I.656, N.660, G.684, A.685, T.688 Ligands: MG.8 14 PLIP interactions: 12 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:G.480, B:G.521, B:C.522, B:C.522, B:G.523, B:K.524, B:T.525, B:T.525, B:L.526, B:N.624, B:N.660, A:R.766, A:R.766 Salt bridges: B:K.524 AGS.9: 16 residues within 4Å: Chain C: D.205, I.206, G.207, P.247, G.248, T.249, G.250, K.251, T.252, L.253, N.348, I.380, H.384, G.408, A.409 Ligands: MG.11 9 PLIP interactions: 9 interactions with chain C Hydrogen bonds: C:G.207, C:G.248, C:T.249, C:T.249, C:G.250, C:K.251, C:T.252, C:L.253 Salt bridges: C:K.251 AGS.10: 20 residues within 4Å: Chain B: R.635, P.636, R.766 Chain C: D.478, I.479, G.480, P.520, G.521, C.522, G.523, K.524, T.525, L.526, N.624, I.656, N.660, G.684, A.685, T.688 Ligands: MG.12 14 PLIP interactions: 12 interactions with chain C, 2 interactions with chain B Hydrogen bonds: C:G.480, C:G.521, C:C.522, C:C.522, C:G.523, C:K.524, C:T.525, C:T.525, C:L.526, C:N.624, C:N.660, B:R.766, B:R.766 Salt bridges: C:K.524 AGS.13: 16 residues within 4Å: Chain D: D.205, I.206, G.207, P.247, G.248, T.249, G.250, K.251, T.252, L.253, N.348, I.380, H.384, G.408, A.409 Ligands: MG.15 9 PLIP interactions: 9 interactions with chain D Hydrogen bonds: D:G.207, D:G.248, D:T.249, D:T.249, D:G.250, D:K.251, D:T.252, D:L.253 Salt bridges: D:K.251 AGS.14: 20 residues within 4Å: Chain C: R.635, P.636, R.766 Chain D: D.478, I.479, G.480, P.520, G.521, C.522, G.523, K.524, T.525, L.526, N.624, I.656, N.660, G.684, A.685, T.688 Ligands: MG.16 15 PLIP interactions: 13 interactions with chain D, 2 interactions with chain C Hydrogen bonds: D:G.480, D:G.521, D:C.522, D:C.522, D:G.523, D:K.524, D:T.525, D:T.525, D:T.525, D:L.526, D:N.624, D:N.660, C:R.766, C:R.766 Salt bridges: D:K.524 AGS.17: 16 residues within 4Å: Chain E: D.205, I.206, G.207, P.247, G.248, T.249, G.250, K.251, T.252, L.253, N.348, I.380, H.384, G.408, A.409 Ligands: MG.19 9 PLIP interactions: 9 interactions with chain E Hydrogen bonds: E:G.207, E:G.248, E:T.249, E:T.249, E:G.250, E:K.251, E:T.252, E:L.253 Salt bridges: E:K.251 AGS.18: 20 residues within 4Å: Chain D: R.635, P.636, R.766 Chain E: D.478, I.479, G.480, P.520, G.521, C.522, G.523, K.524, T.525, L.526, N.624, I.656, N.660, G.684, A.685, T.688 Ligands: MG.20 14 PLIP interactions: 12 interactions with chain E, 2 interactions with chain D Hydrogen bonds: E:G.480, E:G.521, E:C.522, E:C.522, E:G.523, E:K.524, E:T.525, E:T.525, E:L.526, E:N.624, E:N.660, D:R.766, D:R.766 Salt bridges: E:K.524 AGS.21: 16 residues within 4Å: Chain F: D.205, I.206, G.207, P.247, G.248, T.249, G.250, K.251, T.252, L.253, N.348, I.380, H.384, G.408, A.409 Ligands: MG.23 9 PLIP interactions: 9 interactions with chain F Hydrogen bonds: F:G.207, F:G.248, F:T.249, F:T.249, F:G.250, F:K.251, F:T.252, F:L.253 Salt bridges: F:K.251 AGS.22: 20 residues within 4Å: Chain E: R.635, P.636, R.766 Chain F: D.478, I.479, G.480, P.520, G.521, C.522, G.523, K.524, T.525, L.526, N.624, I.656, N.660, G.684, A.685, T.688 Ligands: MG.24 14 PLIP interactions: 12 interactions with chain F, 2 interactions with chain E Hydrogen bonds: F:G.480, F:G.521, F:C.522, F:C.522, F:G.523, F:K.524, F:T.525, F:T.525, F:L.526, F:N.624, F:N.660, E:R.766, E:R.766 Salt bridges: F:K.524

12 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 3 residues within 4Å: Chain A: T.252, D.304 Ligands: AGS.1 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:T.252 MG.4: 3 residues within 4Å: Chain A: T.525, D.577 Ligands: AGS.2 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:T.525 MG.7: 3 residues within 4Å: Chain B: T.252, D.304 Ligands: AGS.5 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:T.252 MG.8: 3 residues within 4Å: Chain B: T.525, D.577 Ligands: AGS.6 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:T.525 MG.11: 3 residues within 4Å: Chain C: T.252, D.304 Ligands: AGS.9 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:T.252 MG.12: 3 residues within 4Å: Chain C: T.525, D.577 Ligands: AGS.10 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:T.525 MG.15: 3 residues within 4Å: Chain D: T.252, D.304 Ligands: AGS.13 1 PLIP interactions: 1 interactions with chain D Metal complexes: D:T.252 MG.16: 3 residues within 4Å: Chain D: T.525, D.577 Ligands: AGS.14 1 PLIP interactions: 1 interactions with chain D Metal complexes: D:T.525 MG.19: 3 residues within 4Å: Chain E: T.252, D.304 Ligands: AGS.17 1 PLIP interactions: 1 interactions with chain E Metal complexes: E:T.252 MG.20: 3 residues within 4Å: Chain E: T.525, D.577 Ligands: AGS.18 1 PLIP interactions: 1 interactions with chain E Metal complexes: E:T.525 MG.23: 3 residues within 4Å: Chain F: T.252, D.304 Ligands: AGS.21 1 PLIP interactions: 1 interactions with chain F Metal complexes: F:T.252 MG.24: 3 residues within 4Å: Chain F: T.525, D.577 Ligands: AGS.22 1 PLIP interactions: 1 interactions with chain F Metal complexes: F:T.525

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