MolNFT v1 · #137050 · protein

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

5VCA · Vcp-like ATPase: “Vcp like ATPase from T. acidophilum (vat)-substrate bound conformation”. Electron microscopy, 20 pockets (best druggability 0.85). MolNFT v1 #137050 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5VCA
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
Pockets: 20 · best druggability 0.85

Structure

electron microscopy · 1 distinct chain · 49% helix, 10% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
P, M, N, O, Q, R	Vcp-like ATPase	protein	544	49% helix, 10% strand	O05209

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	1044	0.85	0.86	167	empty
2	982	0.83	0.84	144	empty
3	1026	0.82	0.84	156	empty
4	979	0.79	0.81	129	empty
5	505	0.79	0.86	119	empty

Interfaces

7 interfaces between chains.

N–O · 1262 Å² buried · 4 hydrogen bonds · protein-protein
M–N · 1131 Å² buried · 0 hydrogen bonds · protein-protein
O–Q · 1040 Å² buried · 2 hydrogen bonds · protein-protein
Q–R · 869 Å² buried · 2 hydrogen bonds · protein-protein
P–M · 597 Å² buried · 0 hydrogen bonds · protein-protein

Compared structures

5VCA · VCP like ATPase from T. acidophilum (VAT)-Substrate bound conformation · the same entry in another collection · chain N against N, TM-score 1.00
O05209 · AlphaFold monomer V2.0 prediction for vcp-like ATPase (O05209) · a predicted model of the same protein · chain P against A, TM-score 0.86

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 5VCA · PDBe 5VCA · UniProt O05209

GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.