MolNFT v1 · #82510 · protein

Argx from sulfolobus tokodaii complexed with ADP

3VPC · Putative acetylornithine deacetylase: “Argx from sulfolobus tokodaii complexed with ADP”. X-ray diffraction, 1 ligand (ADP), 10 pockets (best druggability 0.83). MolNFT v1 #82510 on GenesisL1: 3D structure, binding sites and pockets…

PDB: 3VPC
Type: protein
Length: 1,121 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Putative acetylornithine deacetylase
EC: 3.5.1.16
UniProt: Q970U6
Ligands: ADP
Pockets: 10 · best druggability 0.83

Structure

x-ray diffraction · 2 distinct chains · 38% helix, 26% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, D	Putative acetylornithine deacetylase (EC 3.5.1.16)	protein	282	38% helix, 26% strand	Q970U6
C	Putative acetylornithine deacetylase (EC 3.5.1.16)	protein	275	39% helix, 27% strand	Q970U6

Ligands and binding sites

ADP · Adenosine-5'-diphosphate · ligand · 4 copies · chains A, B, C, D

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

Pockets

10 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	728	0.83	0.87	80	ADP
2	712	0.83	0.87	71	ADP
3	439	0.81	0.88	50	ADP
4	448	0.79	0.87	49	ADP
5	159	0.51	0.79	34	empty

Interfaces

5 interfaces between chains.

C–D · 2071 Å² buried · 26 hydrogen bonds · protein-protein
A–B · 2037 Å² buried · 25 hydrogen bonds · protein-protein
A–D · 1117 Å² buried · 15 hydrogen bonds · protein-protein
B–C · 1014 Å² buried · 11 hydrogen bonds · protein-protein
A–C · 14 Å² buried · 0 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 4 disulfide (disulfide).

Compared structures

3VPC · ArgX from Sulfolobus tokodaii complexed with ADP · the same entry in another collection · chain D against D, TM-score 1.00
Q970U6 · AlphaFold monomer V2.0 prediction for glutamate--lysw ligase argx (Q970U6) · a predicted model of the same protein · chain D against A, TM-score 0.99

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 Q970U6
Elsewhere: RCSB PDB 3VPC · PDBe 3VPC · UniProt Q970U6

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