SMTL ID : 7rli.1

Cryo-EM structure of human p97 bound to CB-5083 and ADP.

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

homo-12-mer

Ligands

12 x JDP: 1-[4-(benzylamino)-7,8-dihydro-5H-pyrano[4,3-d]pyrimidin-2-yl]-2-methyl-1H-indole-4-carboxamide(Non-covalent)

JDP.1: 16 residues within 4Å: Chain A: V.489, D.493, I.494, G.536, C.537, G.538, L.541, S.667, A.670, I.671, A.674, N.675, R.677, G.699, A.700, T.703 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:I.494, A:L.541, A:L.541, A:I.671, A:A.674 Hydrogen bonds: A:G.536, A:A.670, A:R.677 JDP.3: 16 residues within 4Å: Chain B: V.489, D.493, I.494, G.536, C.537, G.538, L.541, S.667, A.670, I.671, A.674, N.675, R.677, G.699, A.700, T.703 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:I.494, B:L.541, B:L.541, B:I.671, B:A.674 Hydrogen bonds: B:G.536, B:A.670, B:R.677 JDP.5: 16 residues within 4Å: Chain C: V.489, D.493, I.494, G.536, C.537, G.538, L.541, S.667, A.670, I.671, A.674, N.675, R.677, G.699, A.700, T.703 8 PLIP interactions: 8 interactions with chain C Hydrophobic interactions: C:I.494, C:L.541, C:L.541, C:I.671, C:A.674 Hydrogen bonds: C:G.536, C:A.670, C:R.677 JDP.7: 16 residues within 4Å: Chain D: V.489, D.493, I.494, G.536, C.537, G.538, L.541, S.667, A.670, I.671, A.674, N.675, R.677, G.699, A.700, T.703 8 PLIP interactions: 8 interactions with chain D Hydrophobic interactions: D:I.494, D:L.541, D:L.541, D:I.671, D:A.674 Hydrogen bonds: D:G.536, D:A.670, D:R.677 JDP.9: 16 residues within 4Å: Chain E: V.489, D.493, I.494, G.536, C.537, G.538, L.541, S.667, A.670, I.671, A.674, N.675, R.677, G.699, A.700, T.703 8 PLIP interactions: 8 interactions with chain E Hydrophobic interactions: E:I.494, E:L.541, E:L.541, E:I.671, E:A.674 Hydrogen bonds: E:G.536, E:A.670, E:R.677 JDP.11: 16 residues within 4Å: Chain F: V.489, D.493, I.494, G.536, C.537, G.538, L.541, S.667, A.670, I.671, A.674, N.675, R.677, G.699, A.700, T.703 8 PLIP interactions: 8 interactions with chain F Hydrophobic interactions: F:I.494, F:L.541, F:L.541, F:I.671, F:A.674 Hydrogen bonds: F:G.536, F:A.670, F:R.677 JDP.13: 16 residues within 4Å: Chain G: V.489, D.493, I.494, G.536, C.537, G.538, L.541, S.667, A.670, I.671, A.674, N.675, R.677, G.699, A.700, T.703 9 PLIP interactions: 9 interactions with chain G Hydrophobic interactions: G:I.494, G:L.541, G:L.541, G:I.671, G:A.674 Hydrogen bonds: G:G.536, G:A.670, G:R.677, G:T.703 JDP.15: 16 residues within 4Å: Chain H: V.489, D.493, I.494, G.536, C.537, G.538, L.541, S.667, A.670, I.671, A.674, N.675, R.677, G.699, A.700, T.703 9 PLIP interactions: 9 interactions with chain H Hydrophobic interactions: H:I.494, H:L.541, H:L.541, H:I.671, H:A.674 Hydrogen bonds: H:G.536, H:A.670, H:R.677, H:T.703 JDP.17: 16 residues within 4Å: Chain I: V.489, D.493, I.494, G.536, C.537, G.538, L.541, S.667, A.670, I.671, A.674, N.675, R.677, G.699, A.700, T.703 9 PLIP interactions: 9 interactions with chain I Hydrophobic interactions: I:I.494, I:L.541, I:L.541, I:I.671, I:A.674 Hydrogen bonds: I:G.536, I:A.670, I:R.677, I:T.703 JDP.19: 16 residues within 4Å: Chain J: V.489, D.493, I.494, G.536, C.537, G.538, L.541, S.667, A.670, I.671, A.674, N.675, R.677, G.699, A.700, T.703 9 PLIP interactions: 9 interactions with chain J Hydrophobic interactions: J:I.494, J:L.541, J:L.541, J:I.671, J:A.674 Hydrogen bonds: J:G.536, J:A.670, J:R.677, J:T.703 JDP.21: 16 residues within 4Å: Chain K: V.489, D.493, I.494, G.536, C.537, G.538, L.541, S.667, A.670, I.671, A.674, N.675, R.677, G.699, A.700, T.703 9 PLIP interactions: 9 interactions with chain K Hydrophobic interactions: K:I.494, K:L.541, K:L.541, K:I.671, K:A.674 Hydrogen bonds: K:G.536, K:A.670, K:R.677, K:T.703 JDP.23: 16 residues within 4Å: Chain L: V.489, D.493, I.494, G.536, C.537, G.538, L.541, S.667, A.670, I.671, A.674, N.675, R.677, G.699, A.700, T.703 9 PLIP interactions: 9 interactions with chain L Hydrophobic interactions: L:I.494, L:L.541, L:L.541, L:I.671, L:A.674 Hydrogen bonds: L:G.536, L:A.670, L:R.677, L:T.703

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

ADP.2: 16 residues within 4Å: Chain A: D.220, I.221, G.222, P.262, G.263, T.264, G.265, K.266, T.267, L.268, D.319, I.395, H.399, G.423, A.424, A.427 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:G.222, A:G.263, A:T.264, A:G.265, A:K.266, A:T.267, A:T.267, A:D.319 Salt bridges: A:K.266 ADP.4: 16 residues within 4Å: Chain B: D.220, I.221, G.222, P.262, G.263, T.264, G.265, K.266, T.267, L.268, D.319, I.395, H.399, G.423, A.424, A.427 9 PLIP interactions: 9 interactions with chain B Hydrogen bonds: B:G.222, B:G.263, B:T.264, B:G.265, B:K.266, B:T.267, B:T.267, B:D.319 Salt bridges: B:K.266 ADP.6: 15 residues within 4Å: Chain C: D.220, G.222, P.262, G.263, T.264, G.265, K.266, T.267, L.268, D.319, I.395, H.399, G.423, A.424, A.427 9 PLIP interactions: 9 interactions with chain C Hydrogen bonds: C:G.222, C:G.263, C:T.264, C:G.265, C:K.266, C:T.267, C:T.267, C:D.319 Salt bridges: C:K.266 ADP.8: 15 residues within 4Å: Chain D: D.220, G.222, P.262, G.263, T.264, G.265, K.266, T.267, L.268, D.319, I.395, H.399, G.423, A.424, A.427 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:D.319 Salt bridges: D:K.266 ADP.10: 16 residues within 4Å: Chain E: D.220, I.221, G.222, P.262, G.263, T.264, G.265, K.266, T.267, L.268, D.319, I.395, H.399, G.423, A.424, A.427 9 PLIP interactions: 9 interactions with chain E Hydrogen bonds: E:G.222, E:G.263, E:T.264, E:G.265, E:K.266, E:T.267, E:T.267, E:D.319 Salt bridges: E:K.266 ADP.12: 16 residues within 4Å: Chain F: D.220, I.221, G.222, C.224, G.263, T.264, G.265, K.266, T.267, L.268, D.319, I.395, H.399, G.423, A.424, A.427 9 PLIP interactions: 9 interactions with chain F Hydrogen bonds: F:G.222, F:G.263, F:T.264, F:G.265, F:K.266, F:T.267, F:T.267, F:D.319 Salt bridges: F:K.266 ADP.14: 17 residues within 4Å: Chain G: D.220, I.221, G.222, P.262, G.263, T.264, G.265, K.266, T.267, L.268, D.319, I.395, I.398, H.399, G.423, A.424, A.427 8 PLIP interactions: 8 interactions with chain G Hydrogen bonds: G:G.222, G:G.263, G:T.264, G:G.265, G:K.266, G:T.267, G:T.267 Salt bridges: G:K.266 ADP.16: 15 residues within 4Å: Chain H: D.220, G.222, P.262, G.263, T.264, G.265, K.266, T.267, L.268, D.319, I.395, H.399, G.423, A.424, A.427 7 PLIP interactions: 7 interactions with chain H Hydrogen bonds: H:G.222, H:G.263, H:T.264, H:G.265, H:K.266, H:T.267 Salt bridges: H:K.266 ADP.18: 16 residues within 4Å: Chain I: D.220, I.221, G.222, P.262, G.263, T.264, G.265, K.266, T.267, L.268, D.319, I.395, H.399, G.423, A.424, A.427 8 PLIP interactions: 8 interactions with chain I Hydrogen bonds: I:G.222, I:G.263, I:T.264, I:T.264, I:G.265, I:K.266, I:T.267 Salt bridges: I:K.266 ADP.20: 16 residues within 4Å: Chain J: D.220, I.221, G.222, P.262, G.263, T.264, G.265, K.266, T.267, L.268, D.319, I.395, H.399, G.423, A.424, A.427 8 PLIP interactions: 8 interactions with chain J Hydrogen bonds: J:G.222, J:G.263, J:T.264, J:G.265, J:K.266, J:T.267, J:T.267 Salt bridges: J:K.266 ADP.22: 16 residues within 4Å: Chain K: D.220, I.221, G.222, P.262, G.263, T.264, G.265, K.266, T.267, L.268, D.319, I.395, H.399, G.423, A.424, A.427 7 PLIP interactions: 7 interactions with chain K Hydrogen bonds: K:G.222, K:G.263, K:T.264, K:G.265, K:K.266, K:T.267 Salt bridges: K:K.266 ADP.24: 16 residues within 4Å: Chain L: D.220, G.222, P.262, G.263, T.264, G.265, K.266, T.267, L.268, D.319, I.395, I.398, H.399, G.423, A.424, A.427 9 PLIP interactions: 9 interactions with chain L Hydrogen bonds: L:G.222, L:G.263, L:T.264, L:T.264, L:G.265, L:K.266, L:T.267, L:T.267 Salt bridges: L:K.266

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: ABCDEFGHIJKL

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

G
G

H
H

I
I

J
J

K
K

L
L

Transitional endoplasmic reticulum ATPase