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Structure of P97/VCP in complex with ADP

Analyse Structure of P97/VCP in complex with ADP in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3CF3
Type: protein
Length: 2,169 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Transitional endoplasmic reticulum ATPase
UniProt: Q01853
Ligands: ADP
Pockets: 20 · best druggability 0.82

Structure

x-ray diffraction · 1 distinct chain · 38% helix, 16% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C	Transitional endoplasmic reticulum ATPase	protein	723	38% helix, 16% strand	Q01853

Ligands and binding sites

ADP · Adenosine-5'-diphosphate · ligand · 6 copies · chains A, B, C

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	658	0.82	0.86	86	empty
2	667	0.81	0.86	87	empty
3	348	0.74	0.85	66	ADP
4	990	0.73	0.77	77	ADP
5	222	0.71	0.87	39	empty

Interfaces

3 interfaces between chains.

A–B · 3223 Å² buried · 25 hydrogen bonds · protein-protein
B–C · 3134 Å² buried · 27 hydrogen bonds · protein-protein
A–C · 13 Å² buried · 0 hydrogen bonds · protein-protein

Compared structures

3CF3 · Structure of P97/vcp in complex with ADP · the same entry in another collection · chain A against A, TM-score 1.00
Q01853 · AlphaFold monomer V2.0 prediction for transitional endoplasmic reticulum ATPase (Q01853) · a predicted model of the same protein · chain A against A, TM-score 0.76

Analyse

Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
Every structure of UniProt Q01853
Elsewhere: RCSB PDB 3CF3 · PDBe 3CF3 · UniProt Q01853

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