SMTL ID : 7jy5.1

Structure of human p97 in complex with ATPgammaS and Npl4/Ufd1 (masked around p97)

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

homo-hexamer

Ligands

12 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 4 residues within 4Å: Chain A: T.252, D.304, E.305 Ligands: AGS.3 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:T.252 MG.2: 3 residues within 4Å: Chain A: T.525, D.577 Ligands: AGS.4 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:T.525 MG.5: 4 residues within 4Å: Chain B: T.252, D.304, E.305 Ligands: AGS.7 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:T.252 MG.6: 3 residues within 4Å: Chain B: T.525, D.577 Ligands: AGS.8 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:T.525 MG.9: 4 residues within 4Å: Chain C: T.252, D.304, E.305 Ligands: AGS.11 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:T.252 MG.10: 3 residues within 4Å: Chain C: T.525, D.577 Ligands: AGS.12 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:T.525 MG.13: 4 residues within 4Å: Chain D: T.252, D.304, E.305 Ligands: AGS.15 1 PLIP interactions: 1 interactions with chain D Metal complexes: D:T.252 MG.14: 3 residues within 4Å: Chain D: T.525, D.577 Ligands: AGS.16 1 PLIP interactions: 1 interactions with chain D Metal complexes: D:T.525 MG.17: 4 residues within 4Å: Chain E: T.252, D.304, E.305 Ligands: AGS.19 1 PLIP interactions: 1 interactions with chain E Metal complexes: E:T.252 MG.18: 3 residues within 4Å: Chain E: T.525, D.577 Ligands: AGS.20 1 PLIP interactions: 1 interactions with chain E Metal complexes: E:T.525 MG.21: 4 residues within 4Å: Chain F: T.252, D.304, E.305 Ligands: AGS.23 1 PLIP interactions: 1 interactions with chain F Metal complexes: F:T.252 MG.22: 3 residues within 4Å: Chain F: T.525, D.577 Ligands: AGS.24 1 PLIP interactions: 1 interactions with chain F Metal complexes: F:T.525

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

AGS.3: 18 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 Chain F: R.359, F.360 Ligands: MG.1 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.4: 19 residues within 4Å: Chain A: D.478, I.479, G.480, 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.2 13 PLIP interactions: 10 interactions with chain A, 3 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:L.526, A:T.688, F:R.635, F:R.766, F:R.766 Salt bridges: A:K.524 AGS.7: 18 residues within 4Å: Chain A: R.359, F.360 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.5 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.8: 19 residues within 4Å: Chain A: R.635, P.636, R.766 Chain B: D.478, I.479, G.480, 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.6 14 PLIP interactions: 11 interactions with chain B, 3 interactions with chain A Hydrogen bonds: B:G.480, B:G.521, B:C.522, B:C.522, B:G.523, B:G.523, B:K.524, B:T.525, B:L.526, B:T.688, A:R.635, A:R.766, A:R.766 Salt bridges: B:K.524 AGS.11: 18 residues within 4Å: Chain B: R.359, F.360 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.9 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.12: 19 residues within 4Å: Chain B: R.635, P.636, R.766 Chain C: D.478, I.479, G.480, 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.10 13 PLIP interactions: 10 interactions with chain C, 3 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:L.526, C:T.688, B:R.635, B:R.766, B:R.766 Salt bridges: C:K.524 AGS.15: 18 residues within 4Å: Chain C: R.359, F.360 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.13 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.16: 19 residues within 4Å: Chain C: R.635, P.636, R.766 Chain D: D.478, I.479, G.480, 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.14 13 PLIP interactions: 10 interactions with chain D, 3 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:L.526, D:T.688, C:R.635, C:R.766, C:R.766 Salt bridges: D:K.524 AGS.19: 18 residues within 4Å: Chain D: R.359, F.360 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.17 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.20: 19 residues within 4Å: Chain D: R.635, P.636, R.766 Chain E: D.478, I.479, G.480, 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.18 14 PLIP interactions: 11 interactions with chain E, 3 interactions with chain D Hydrogen bonds: E:G.480, E:G.521, E:C.522, E:C.522, E:G.523, E:G.523, E:K.524, E:T.525, E:L.526, E:T.688, D:R.635, D:R.766, D:R.766 Salt bridges: E:K.524 AGS.23: 18 residues within 4Å: Chain E: R.359, F.360 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.21 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.24: 19 residues within 4Å: Chain E: R.635, P.636, R.766 Chain F: D.478, I.479, G.480, 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.22 13 PLIP interactions: 10 interactions with chain F, 3 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:L.526, F:T.688, E:R.635, E:R.766, E:R.766 Salt bridges: F:K.524

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Pan, M. et al., Seesaw conformations of Npl4 in the human p97 complex and the inhibitory mechanism of a disulfiram derivative. Nat Commun (2021)

Release Date

2021-01-20

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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