SMTL ID : 5dyi.1 (1 other biounit)

Structure of p97 N-D1 wild-type in complex with ADP

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 3.71 Å

Oligo State

homo-hexamer

Ligands

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

ADP.1: 16 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, D.304, I.380, H.384, G.408, A.409 Chain B: R.359 13 PLIP interactions: 1 interactions with chain B, 12 interactions with chain A Salt bridges: B:R.359, A:K.251 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, A:T.252, A:L.253, A:G.408 ADP.2: 16 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, D.304, I.380, H.384, G.408, A.409 Chain C: R.359 12 PLIP interactions: 11 interactions with chain B, 1 interactions with chain C 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, B:T.252, B:L.253 Salt bridges: B:K.251, C:R.359 ADP.3: 15 residues within 4Å: Chain C: D.205, I.206, G.207, G.248, T.249, G.250, K.251, T.252, L.253, D.304, I.380, H.384, G.408, A.409 Chain D: R.359 11 PLIP interactions: 10 interactions with chain C, 1 interactions with chain D 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, C:L.253 Salt bridges: C:K.251, D:R.359 ADP.4: 15 residues within 4Å: Chain D: D.205, I.206, G.207, G.248, T.249, G.250, K.251, T.252, L.253, D.304, I.380, H.384, G.408, A.409 Chain E: R.359 11 PLIP interactions: 1 interactions with chain E, 10 interactions with chain D Salt bridges: E:R.359, D:K.251 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, D:L.253 ADP.5: 16 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, D.304, I.380, H.384, G.408, A.409 Chain F: R.359 10 PLIP interactions: 9 interactions with chain E, 1 interactions with chain F Hydrogen bonds: E:G.207, E:G.207, E:G.248, E:T.249, E:G.250, E:K.251, E:T.252, E:L.253 Salt bridges: E:K.251, F:R.359 ADP.6: 16 residues within 4Å: Chain A: R.359 Chain F: D.205, I.206, G.207, P.247, G.248, T.249, G.250, K.251, T.252, L.253, D.304, I.380, H.384, G.408, A.409 13 PLIP interactions: 12 interactions with chain F, 1 interactions with chain A 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, F:T.252, F:L.253, F:D.304 Salt bridges: F:K.251, A:R.359

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Tang, W.K. et al., Role of the D1-D2 Linker of Human VCP/p97 in the Asymmetry and ATPase Activity of the D1-domain. Sci Rep (2016)

Release Date

2016-02-10

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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