SMTL ID : 8uvo.1

Human p97/VCP R155H mutant structure with a triazole inhibitor (NSC804515)

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-hexamer

Ligands

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

ADP.1: 14 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, I.380, H.384, G.408, A.409 9 PLIP interactions: 9 interactions with chain A 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 Salt bridges: A:K.251 ADP.2: 15 residues within 4Å: Chain A: D.478, I.479, G.480, L.482, G.521, C.522, G.523, K.524, T.525, L.526, D.577, N.624, I.656, N.660, G.684 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:G.480, A:G.521, A:C.522, A:C.522, A:G.523, A:K.524, A:T.525, A:N.624, A:N.660, A:T.688 ADP.4: 14 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, I.380, H.384, G.408, A.409 9 PLIP interactions: 9 interactions with chain B Hydrogen bonds: B:G.207, B:G.207, B:G.248, B:T.249, B:G.250, B:K.251, B:T.252, B:T.252 Salt bridges: B:K.251 ADP.5: 15 residues within 4Å: Chain B: D.478, I.479, G.480, L.482, P.520, G.521, C.522, G.523, K.524, T.525, L.526, D.577, I.656, N.660, G.684 10 PLIP interactions: 10 interactions with chain B Hydrogen bonds: B:G.480, B:G.521, B:C.522, B:C.522, B:G.523, B:K.524, B:T.525, B:N.624, B:N.660, B:T.688 ADP.7: 14 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, I.380, H.384, G.408, A.409 9 PLIP interactions: 9 interactions with chain C Hydrogen bonds: C:G.207, C:G.207, C:G.248, C:T.249, C:G.250, C:K.251, C:T.252, C:T.252 Salt bridges: C:K.251 ADP.8: 14 residues within 4Å: Chain C: D.478, I.479, G.480, L.482, G.521, C.522, G.523, K.524, T.525, L.526, D.577, I.656, N.660, G.684 10 PLIP interactions: 10 interactions with chain C Hydrogen bonds: C:G.480, C:G.521, C:C.522, C:C.522, C:G.523, C:K.524, C:T.525, C:N.624, C:N.660, C:T.688 ADP.10: 14 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, I.380, H.384, G.408, A.409 9 PLIP interactions: 9 interactions with chain D Hydrogen bonds: D:G.207, D:G.207, D:G.248, D:T.249, D:G.250, D:K.251, D:T.252, D:T.252 Salt bridges: D:K.251 ADP.11: 15 residues within 4Å: Chain D: D.478, I.479, G.480, L.482, G.521, C.522, G.523, K.524, T.525, L.526, D.577, N.624, I.656, N.660, G.684 10 PLIP interactions: 10 interactions with chain D Hydrogen bonds: D:G.480, D:G.521, D:C.522, D:C.522, D:G.523, D:K.524, D:T.525, D:N.624, D:N.660, D:T.688 ADP.13: 14 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, I.380, H.384, G.408, A.409 9 PLIP interactions: 9 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 Salt bridges: E:K.251 ADP.14: 15 residues within 4Å: Chain E: D.478, I.479, G.480, L.482, P.520, G.521, C.522, G.523, K.524, T.525, L.526, D.577, I.656, N.660, G.684 10 PLIP interactions: 10 interactions with chain E Hydrogen bonds: E:G.480, E:G.521, E:C.522, E:C.522, E:G.523, E:K.524, E:T.525, E:N.624, E:N.660, E:T.688 ADP.16: 14 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, I.380, H.384, G.408, A.409 9 PLIP interactions: 9 interactions with chain F Hydrogen bonds: F:G.207, F:G.207, F:G.248, F:T.249, F:G.250, F:K.251, F:T.252, F:T.252 Salt bridges: F:K.251 ADP.17: 14 residues within 4Å: Chain F: D.478, I.479, G.480, L.482, G.521, C.522, G.523, K.524, T.525, L.526, D.577, I.656, N.660, G.684 10 PLIP interactions: 10 interactions with chain F Hydrogen bonds: F:G.480, F:G.521, F:C.522, F:C.522, F:G.523, F:K.524, F:T.525, F:N.624, F:N.660, F:T.688

6 x XNU: N-[3-(2,5-difluoro-4-{[(4M)-5-(hexylsulfanyl)-4-(pyridin-3-yl)-4H-1,2,4-triazol-3-yl]methoxy}phenyl)prop-2-yn-1-yl]propanamide(Non-covalent)

XNU.3: 17 residues within 4Å: Chain A: L.492, V.493, P.496, V.497, P.500, L.504, P.510, S.511, K.512, C.535, A.537, C.572, V.573, K.615, N.616, F.618 Chain F: K.663 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:V.493, A:L.504, A:P.510, A:K.512, A:A.537, A:V.573, A:F.618 pi-Cation interactions: A:K.615 Halogen bonds: A:P.500 XNU.6: 17 residues within 4Å: Chain A: K.663 Chain B: L.492, V.493, P.496, V.497, P.500, L.504, P.510, S.511, K.512, C.535, A.537, C.572, V.573, K.615, N.616, F.618 9 PLIP interactions: 9 interactions with chain B Hydrophobic interactions: B:V.493, B:L.504, B:P.510, B:K.512, B:A.537, B:V.573, B:F.618 pi-Cation interactions: B:K.615 Halogen bonds: B:P.500 XNU.9: 17 residues within 4Å: Chain B: K.663 Chain C: L.492, V.493, P.496, V.497, P.500, L.504, P.510, S.511, K.512, C.535, A.537, C.572, V.573, K.615, N.616, F.618 9 PLIP interactions: 9 interactions with chain C Hydrophobic interactions: C:V.493, C:L.504, C:P.510, C:K.512, C:A.537, C:V.573, C:F.618 pi-Cation interactions: C:K.615 Halogen bonds: C:P.500 XNU.12: 17 residues within 4Å: Chain C: K.663 Chain D: L.492, V.493, P.496, V.497, P.500, L.504, P.510, S.511, K.512, C.535, A.537, C.572, V.573, K.615, N.616, F.618 9 PLIP interactions: 9 interactions with chain D Hydrophobic interactions: D:V.493, D:L.504, D:P.510, D:K.512, D:A.537, D:V.573, D:F.618 pi-Cation interactions: D:K.615 Halogen bonds: D:P.500 XNU.15: 17 residues within 4Å: Chain D: K.663 Chain E: L.492, V.493, P.496, V.497, P.500, L.504, P.510, S.511, K.512, C.535, A.537, C.572, V.573, K.615, N.616, F.618 9 PLIP interactions: 9 interactions with chain E Hydrophobic interactions: E:V.493, E:L.504, E:P.510, E:K.512, E:A.537, E:V.573, E:F.618 pi-Cation interactions: E:K.615 Halogen bonds: E:P.500 XNU.18: 17 residues within 4Å: Chain E: K.663 Chain F: L.492, V.493, P.496, V.497, P.500, L.504, P.510, S.511, K.512, C.535, A.537, C.572, V.573, K.615, N.616, F.618 9 PLIP interactions: 9 interactions with chain F Hydrophobic interactions: F:V.493, F:L.504, F:P.510, F:K.512, F:A.537, F:V.573, F:F.618 pi-Cation interactions: F:K.615 Halogen bonds: F:P.500

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Nandi, P. et al., Mechanism of allosteric inhibition of human p97/VCP ATPase and its disease mutant by triazole inhibitors. Commun Chem (2024)

Release Date

2024-08-21

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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