SMTL ID : 8vls.1

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

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-12-mer

Ligands

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

01.1: 7 residues within 4Å: Chain A: R.625, D.627, D.751, K.754, Y.755, M.757, F.758 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:K.754, A:K.754, A:Y.755, A:M.757, A:F.758 Hydrogen bonds: A:D.627 01.2: 7 residues within 4Å: Chain B: R.625, D.627, D.751, K.754, Y.755, M.757, F.758 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:K.754, B:K.754, B:Y.755, B:M.757, B:F.758 Hydrogen bonds: B:D.627, B:D.627 01.3: 7 residues within 4Å: Chain C: R.625, D.627, D.751, K.754, Y.755, M.757, F.758 7 PLIP interactions: 7 interactions with chain C Hydrophobic interactions: C:K.754, C:K.754, C:Y.755, C:M.757, C:F.758 Hydrogen bonds: C:D.627, C:D.627 01.4: 7 residues within 4Å: Chain D: R.625, D.627, D.751, K.754, Y.755, M.757, F.758 6 PLIP interactions: 6 interactions with chain D Hydrophobic interactions: D:K.754, D:K.754, D:Y.755, D:M.757, D:F.758 Hydrogen bonds: D:D.627 01.5: 7 residues within 4Å: Chain E: R.625, D.627, D.751, K.754, Y.755, M.757, F.758 7 PLIP interactions: 7 interactions with chain E Hydrophobic interactions: E:K.754, E:K.754, E:Y.755, E:M.757, E:F.758 Hydrogen bonds: E:D.627, E:D.627 01.6: 7 residues within 4Å: Chain F: R.625, D.627, D.751, K.754, Y.755, M.757, F.758 6 PLIP interactions: 6 interactions with chain F Hydrophobic interactions: F:K.754, F:K.754, F:Y.755, F:M.757, F:F.758 Hydrogen bonds: F:D.627 01.7: 7 residues within 4Å: Chain G: R.625, D.627, D.751, K.754, Y.755, M.757, F.758 5 PLIP interactions: 5 interactions with chain G Hydrophobic interactions: G:K.754, G:K.754, G:Y.755, G:F.758 Hydrogen bonds: G:D.627 01.8: 7 residues within 4Å: Chain H: R.625, D.627, D.751, K.754, Y.755, M.757, F.758 5 PLIP interactions: 5 interactions with chain H Hydrophobic interactions: H:K.754, H:K.754, H:Y.755, H:F.758 Hydrogen bonds: H:D.627 01.9: 7 residues within 4Å: Chain I: R.625, D.627, D.751, K.754, Y.755, M.757, F.758 6 PLIP interactions: 6 interactions with chain I Hydrophobic interactions: I:K.754, I:K.754, I:Y.755, I:M.757, I:F.758 Hydrogen bonds: I:D.627 01.10: 7 residues within 4Å: Chain J: R.625, D.627, D.751, K.754, Y.755, M.757, F.758 6 PLIP interactions: 6 interactions with chain J Hydrophobic interactions: J:K.754, J:K.754, J:Y.755, J:M.757, J:F.758 Hydrogen bonds: J:D.627 01.11: 7 residues within 4Å: Chain K: R.625, D.627, D.751, K.754, Y.755, M.757, F.758 6 PLIP interactions: 6 interactions with chain K Hydrophobic interactions: K:K.754, K:K.754, K:Y.755, K:F.758 Hydrogen bonds: K:R.625, K:D.627 01.12: 7 residues within 4Å: Chain L: R.625, D.627, D.751, K.754, Y.755, M.757, F.758 6 PLIP interactions: 6 interactions with chain L Hydrophobic interactions: L:K.754, L:K.754, L:Y.755, L:M.757, L:F.758 Hydrogen bonds: L:D.627

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: 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

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