SMTL ID : 7mhs.1

Structure of p97 (subunits A to E) with substrate engaged

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY 3.60 Å

Oligo State

hetero-5-1-mer

Ligands

10 x ADP: ADENOSINE-5'-DIPHOSPHATE(Non-covalent)

ADP.1: 16 residues within 4Å: Chain A: D.478, G.480, G.521, C.522, G.523, K.524, T.525, L.526, I.656, N.660, G.684, A.685, T.688 Chain B: R.635 Ligands: BEF.2, MG.3 13 PLIP interactions: 11 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:G.480, A:G.480, A:G.521, A:C.522, A:G.523, A:T.525, A:T.525, A:T.525, A:L.526 Salt bridges: A:K.524, A:K.524, B:R.635, B:R.635 ADP.4: 16 residues within 4Å: Chain A: I.206, G.207, G.248, T.249, G.250, K.251, T.252, L.253, R.256, I.380, H.384, A.409 Chain B: R.359, R.362 Ligands: BEF.5, MG.6 14 PLIP interactions: 11 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:G.207, A:G.207, A:G.248, A:T.249, A:G.250, A:K.251, A:T.252, A:T.252, A:L.253, A:R.256, B:R.362 Salt bridges: A:K.251, B:R.359, B:R.359 ADP.7: 18 residues within 4Å: Chain B: D.478, I.479, G.480, G.521, C.522, G.523, K.524, T.525, L.526, I.656, G.684, A.685, T.688 Chain C: D.609, R.635, R.638 Ligands: BEF.8, MG.9 12 PLIP interactions: 9 interactions with chain B, 3 interactions with chain C Hydrogen bonds: B:G.480, B:G.521, B:C.522, B:G.523, B:K.524, B:T.525, B:L.526 Salt bridges: B:K.524, B:K.524, C:R.635, C:R.635, C:R.638 ADP.10: 17 residues within 4Å: Chain B: D.205, I.206, G.207, G.248, T.249, G.250, T.252, L.253, R.256, I.380, H.384, A.409 Chain C: D.333, R.359, R.362 Ligands: BEF.11, MG.12 11 PLIP interactions: 8 interactions with chain B, 3 interactions with chain C Hydrogen bonds: B:G.207, B:G.207, B:G.248, B:T.249, B:G.250, B:T.252, B:L.253, B:R.256 Salt bridges: C:R.359, C:R.359, C:R.362 ADP.13: 16 residues within 4Å: Chain C: D.478, I.479, G.480, G.521, C.522, G.523, K.524, T.525, L.526, I.656, G.684, A.685 Chain D: R.635, R.638 Ligands: BEF.14, MG.15 12 PLIP interactions: 9 interactions with chain C, 3 interactions with chain D Hydrogen bonds: C:G.480, C:G.480, C:G.521, C:C.522, C:G.523, C:T.525, C:L.526 Salt bridges: C:K.524, C:K.524, D:R.635, D:R.635, D:R.638 ADP.16: 16 residues within 4Å: Chain C: D.205, G.207, G.248, T.249, G.250, K.251, T.252, L.253, R.256, H.384, A.409 Chain D: D.333, R.359, R.362 Ligands: BEF.17, MG.18 11 PLIP interactions: 8 interactions with chain C, 3 interactions with chain D Hydrogen bonds: C:G.207, C:G.248, C:T.249, C:G.250, C:T.252, C:L.253, C:R.256, D:R.362 Salt bridges: C:K.251, D:R.359, D:R.359 ADP.19: 17 residues within 4Å: Chain D: D.478, I.479, G.480, P.520, G.521, C.522, G.523, K.524, T.525, L.526, I.656, G.684, A.685 Chain E: R.635, R.638 Ligands: BEF.20, MG.21 13 PLIP interactions: 11 interactions with chain D, 2 interactions with chain E Hydrogen bonds: D:G.480, D:G.480, D:G.521, D:C.522, D:G.523, D:K.524, D:T.525, D:T.525, D:L.526, E:R.638 Salt bridges: D:K.524, D:K.524, E:R.635 ADP.22: 18 residues within 4Å: Chain D: D.205, I.206, G.207, G.248, T.249, G.250, K.251, T.252, L.253, I.380, I.383, H.384, A.409 Chain E: D.333, R.359, R.362 Ligands: BEF.23, MG.24 10 PLIP interactions: 7 interactions with chain D, 3 interactions with chain E Hydrogen bonds: D:G.207, D:G.248, D:T.249, D:T.249, D:G.250, D:T.252, D:L.253 Salt bridges: E:R.359, E:R.359, E:R.362 ADP.25: 14 residues within 4Å: Chain E: D.478, I.479, G.480, G.521, C.522, G.523, K.524, T.525, L.526, I.656, N.660, G.684, A.685, T.688 9 PLIP interactions: 9 interactions with chain E Hydrogen bonds: E:D.478, E:G.480, E:G.521, E:G.523, E:T.525, E:T.525, E:T.525, E:L.526, E:N.660 ADP.26: 12 residues within 4Å: Chain E: D.205, G.207, G.248, T.249, G.250, K.251, T.252, L.253, D.304, I.380, G.408, A.409 11 PLIP interactions: 11 interactions with chain E Hydrogen bonds: E:G.207, E:G.207, E:G.248, E:T.249, E:G.250, E:K.251, E:T.252, E:T.252, E:L.253 Salt bridges: E:K.251, E:K.251

8 x BEF: BERYLLIUM TRIFLUORIDE ION(Non-covalent)

BEF.2: 6 residues within 4Å: Chain A: P.520, N.624 Chain B: R.635, R.638 Ligands: ADP.1, MG.3 No protein-ligand interaction detected (PLIP) BEF.5: 10 residues within 4Å: Chain A: P.246, P.247, G.248, K.251, E.305, N.348 Chain B: R.359, R.362 Ligands: ADP.4, MG.6 No protein-ligand interaction detected (PLIP) BEF.8: 7 residues within 4Å: Chain B: P.520, K.524, N.624 Chain C: R.635, R.638 Ligands: ADP.7, MG.9 No protein-ligand interaction detected (PLIP) BEF.11: 10 residues within 4Å: Chain B: P.246, P.247, G.248, K.251, E.305, N.348 Chain C: R.359, R.362 Ligands: ADP.10, MG.12 No protein-ligand interaction detected (PLIP) BEF.14: 8 residues within 4Å: Chain C: P.520, G.521, K.524, N.624 Chain D: R.635, R.638 Ligands: ADP.13, MG.15 No protein-ligand interaction detected (PLIP) BEF.17: 8 residues within 4Å: Chain C: P.247, G.248, K.251, T.252, E.305 Chain D: R.362 Ligands: ADP.16, MG.18 No protein-ligand interaction detected (PLIP) BEF.20: 9 residues within 4Å: Chain D: P.520, G.521, K.524, E.578, N.624 Chain E: R.635, R.638 Ligands: ADP.19, MG.21 No protein-ligand interaction detected (PLIP) BEF.23: 8 residues within 4Å: Chain D: P.247, G.248, K.251, E.305 Chain E: R.359, R.362 Ligands: ADP.22, MG.24 No protein-ligand interaction detected (PLIP)

8 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 4 residues within 4Å: Chain A: T.525, D.577 Ligands: ADP.1, BEF.2 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:T.525 MG.6: 5 residues within 4Å: Chain A: T.252, E.305 Chain B: R.362 Ligands: ADP.4, BEF.5 No protein-ligand interaction detected (PLIP) MG.9: 4 residues within 4Å: Chain B: T.525, E.578 Ligands: ADP.7, BEF.8 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:T.525 MG.12: 4 residues within 4Å: Chain B: T.252 Chain C: R.362 Ligands: ADP.10, BEF.11 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:T.252 MG.15: 5 residues within 4Å: Chain C: T.525 Chain D: D.609, R.638 Ligands: ADP.13, BEF.14 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:T.525 MG.18: 4 residues within 4Å: Chain C: T.252, D.304 Ligands: ADP.16, BEF.17 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:T.252 MG.21: 3 residues within 4Å: Chain D: T.525 Ligands: ADP.19, BEF.20 1 PLIP interactions: 1 interactions with chain D Metal complexes: D:T.525 MG.24: 6 residues within 4Å: Chain D: T.252, D.304, E.305 Chain E: R.362 Ligands: ADP.22, BEF.23 1 PLIP interactions: 1 interactions with chain D Metal complexes: D:T.252

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Xu, Y. et al., Active conformation of the p97-p47 unfoldase complex. Nat Commun (2022)

Release Date

2022-05-11

Peptides

Transitional endoplasmic reticulum ATPase: ABCDE
Unknown substrate: F

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
G

Transitional endoplasmic reticulum ATPase

Unknown substrate

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