SMTL ID : 8vov.1

Structure of VCP in complex with an ATPase activator and ADP (D2 domains only, hexameric form)

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-hexamer

Ligands

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

ADP.1: 14 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, I.656, N.660, G.684, T.688 11 PLIP interactions: 11 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:T.525, A:N.660, A:T.688 Salt bridges: A:K.524 ADP.3: 14 residues within 4Å: Chain B: D.478, I.479, G.480, P.520, G.521, C.522, G.523, K.524, T.525, L.526, I.656, N.660, G.684, T.688 11 PLIP interactions: 11 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:T.525, B:N.660, B:T.688 Salt bridges: B:K.524 ADP.5: 14 residues within 4Å: Chain C: D.478, I.479, G.480, P.520, G.521, C.522, G.523, K.524, T.525, L.526, I.656, N.660, G.684, T.688 10 PLIP interactions: 10 interactions with chain C Hydrogen bonds: C:G.480, C:G.480, C:G.521, C:C.522, C:G.523, C:K.524, C:T.525, C:N.660, C:T.688 Salt bridges: C:K.524 ADP.7: 14 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, N.660, G.684, T.688 11 PLIP interactions: 11 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:T.525, D:N.660, D:T.688 Salt bridges: D:K.524 ADP.9: 14 residues within 4Å: Chain E: D.478, I.479, G.480, P.520, G.521, C.522, G.523, K.524, T.525, L.526, I.656, N.660, G.684, T.688 11 PLIP interactions: 11 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:T.525, E:N.660, E:T.688 Salt bridges: E:K.524 ADP.11: 14 residues within 4Å: Chain F: D.478, I.479, G.480, P.520, G.521, C.522, G.523, K.524, T.525, L.526, I.656, N.660, G.684, T.688 11 PLIP interactions: 11 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:T.525, F:N.660, F:T.688 Salt bridges: F:K.524

6 x 01: (3R)-N-[2-(ethylsulfanyl)phenyl]-3-(1-oxo-1,3-dihydro-2H-isoindol-2-yl)butanamide

01.2: 7 residues within 4Å: Chain A: R.625, D.627, D.751, K.754, Y.755, M.757, F.758 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:F.758 Hydrogen bonds: A:R.625, A:D.627, A:D.627, A:K.754 01.4: 7 residues within 4Å: Chain B: R.625, D.627, D.751, K.754, Y.755, M.757, F.758 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:F.758 Hydrogen bonds: B:R.625, B:D.627, B:K.754 01.6: 7 residues within 4Å: Chain C: R.625, D.627, D.751, K.754, Y.755, M.757, F.758 5 PLIP interactions: 5 interactions with chain C Hydrophobic interactions: C:F.758 Hydrogen bonds: C:R.625, C:D.627, C:D.627, C:K.754 01.8: 7 residues within 4Å: Chain D: R.625, D.627, D.751, K.754, Y.755, M.757, F.758 5 PLIP interactions: 5 interactions with chain D Hydrophobic interactions: D:F.758 Hydrogen bonds: D:R.625, D:D.627, D:D.627, D:K.754 01.10: 7 residues within 4Å: Chain E: R.625, D.627, D.751, K.754, Y.755, M.757, F.758 4 PLIP interactions: 4 interactions with chain E Hydrophobic interactions: E:F.758 Hydrogen bonds: E:R.625, E:D.627, E:K.754 01.12: 7 residues within 4Å: Chain F: R.625, D.627, D.751, K.754, Y.755, M.757, F.758 5 PLIP interactions: 5 interactions with chain F Hydrophobic interactions: F:F.758 Hydrogen bonds: F:R.625, F:D.627, F:D.627, F:K.754

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Jones, N.H. et al., Allosteric activation of VCP, an AAA unfoldase, by small molecule mimicry. Proc.Natl.Acad.Sci.USA (2024)

Release Date

2024-06-19

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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