SMTL ID : 8fcp.1

Cryo-EM structure of p97:UBXD1 para state

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-6-2-mer

Ligands

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

ADP.1: 15 residues within 4Å: Chain A: D.205, I.206, G.207, G.208, P.247, G.248, T.249, G.250, T.252, L.253, D.304, I.380, H.384, G.408, A.409 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:G.207, A:G.208, A:G.248, A:T.249, A:L.253, A:D.304 ADP.2: 13 residues within 4Å: Chain A: 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 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:G.480, A:G.480, A:G.521, A:G.523, A:K.524, A:T.525, A:T.525, A:T.525, A:L.526, A:T.688 ADP.3: 12 residues within 4Å: Chain B: D.205, I.206, G.207, G.248, T.249, G.250, T.252, L.253, I.380, H.384, G.408, A.409 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:G.207, B:G.248, B:T.249, B:T.252, B:T.252 ADP.4: 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, G.684, A.685, T.688 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:G.480, B:G.480, B:G.521, B:G.523, B:T.525, B:T.525, B:T.525, B:T.688 ADP.5: 14 residues within 4Å: Chain C: D.205, I.206, G.207, G.248, T.249, G.250, K.251, T.252, L.253, I.380, H.384, G.408, A.409 Chain E: R.359 7 PLIP interactions: 6 interactions with chain C, 1 interactions with chain E Hydrogen bonds: C:G.207, C:G.248, C:T.249, C:G.250, C:K.251, C:T.252, E:R.359 ADP.6: 14 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, N.660, G.684, A.685, T.688 10 PLIP interactions: 10 interactions with chain C Hydrogen bonds: C:G.480, C:G.521, C:C.522, C:G.523, C:K.524, C:T.525, C:T.525, C:T.525, C:L.526, C:T.688 ADP.7: 15 residues within 4Å: Chain E: D.205, I.206, G.207, G.208, G.248, T.249, G.250, T.252, L.253, D.304, I.380, H.384, G.408, A.409 Chain F: K.236 10 PLIP interactions: 8 interactions with chain E, 2 interactions with chain F Hydrogen bonds: E:G.207, E:G.208, E:G.248, E:T.249, E:T.252, E:T.252, E:L.253, E:D.304, F:K.236, F:K.236 ADP.8: 13 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, G.684, A.685, T.688 9 PLIP interactions: 9 interactions with chain E Hydrogen bonds: E:G.480, E:G.480, E:G.521, E:G.523, E:T.525, E:T.525, E:T.525, E:L.526, E:T.688 ADP.9: 12 residues within 4Å: Chain F: D.205, I.206, G.207, G.248, T.249, G.250, T.252, L.253, I.380, H.384, G.408, A.409 4 PLIP interactions: 4 interactions with chain F Hydrogen bonds: F:G.207, F:G.248, F:T.249, F:T.252 ADP.10: 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, G.684, A.685, T.688 8 PLIP interactions: 8 interactions with chain F Hydrogen bonds: F:G.480, F:G.480, F:G.521, F:G.523, F:T.525, F:T.525, F:T.525, F:T.688 ADP.11: 14 residues within 4Å: Chain A: R.359 Chain G: D.205, I.206, G.207, G.248, T.249, G.250, K.251, T.252, L.253, I.380, H.384, G.408, A.409 7 PLIP interactions: 6 interactions with chain G, 1 interactions with chain A Hydrogen bonds: G:G.207, G:G.248, G:T.249, G:G.250, G:K.251, G:T.252, A:R.359 ADP.12: 14 residues within 4Å: Chain G: 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 10 PLIP interactions: 10 interactions with chain G Hydrogen bonds: G:G.480, G:G.521, G:C.522, G:G.523, G:K.524, G:T.525, G:T.525, G:T.525, G:L.526, G:T.688

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Braxton, J.R. et al., The p97/VCP adaptor UBXD1 drives AAA+ remodeling and ring opening through multi-domain tethered interactions. Nat.Struct.Mol.Biol. (2023)

Release Date

2023-06-21

Peptides

Transitional endoplasmic reticulum ATPase: ABCEFG
UBX domain-containing protein 6: DH

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
E

B
D

C
C

E
B

F
A

G
F

D
H

H
G

Transitional endoplasmic reticulum ATPase

UBX domain-containing protein 6

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