Research workbench

Vcp like ATPase from T. acidophilum (vat) - conformation 1

Analyse Vcp like ATPase from T. acidophilum (vat) - conformation 1 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5VC7
Type: protein
Length: 3,264 residues
Chains: 6
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Vcp-like ATPase
UniProt: O05209
Ligands: ATP
Pockets: 20 · best druggability 0.82

Structure

electron microscopy · 1 distinct chain · 47% helix, 9% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, C, D, E, F, G	Vcp-like ATPase	protein	544	47% helix, 9% strand	O05209

Ligands and binding sites

ATP · Adenosine-5'-triphosphate · ligand · 12 copies · chains A, G, C, D, E, F

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	1032	0.82	0.83	129	ATP
2	1096	0.82	0.83	131	ATP
3	1000	0.81	0.83	117	ATP
4	993	0.81	0.82	127	ATP
5	1116	0.81	0.82	134	ATP

Interfaces

6 interfaces between chains.

A–G · 2152 Å² buried · 18 hydrogen bonds · protein-protein
F–G · 2149 Å² buried · 18 hydrogen bonds · protein-protein
C–D · 2149 Å² buried · 18 hydrogen bonds · protein-protein
E–F · 2146 Å² buried · 18 hydrogen bonds · protein-protein
D–E · 2141 Å² buried · 18 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 6 covalent (covalent ligand).

Compared structures

5VC7 · VCP like ATPase from T. acidophilum (VAT) - conformation 1 · the same entry in another collection · chain D against D, TM-score 1.00
O05209 · AlphaFold monomer V2.0 prediction for vcp-like ATPase (O05209) · a predicted model of the same protein · chain A against A, TM-score 0.80

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 O05209
Elsewhere: RCSB PDB 5VC7 · PDBe 5VC7 · UniProt O05209

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