MolNFT v1 · #82052 · protein

Crystal structure of dnpep, znmg form

3VAT · Aspartyl aminopeptidase: “Crystal structure of dnpep, znmg form”. X-ray diffraction, 2 ligands (ZN, MG), 3 pockets (best druggability 0.46). MolNFT v1 #82052 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 3VAT
Type: protein
Length: 458 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Aspartyl aminopeptidase
EC: 3.4.11.21
UniProt: Q2HJH1
Ligands: ZN, MG
Pockets: 3 · best druggability 0.46

Structure

x-ray diffraction · 1 distinct chain · 33% helix, 26% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Aspartyl aminopeptidase (EC 3.4.11.21)	protein	458	33% helix, 26% strand	Q2HJH1

Ligands and binding sites

ZN · Zinc ion · metal · chains A
MG · Magnesium ion · metal · chains A

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

Pockets

3 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	150	0.46	0.77	20	empty
2	114	0.45	0.78	17	ZN
3	52	0.28	0.74	15	empty

Compared structures

3VAT · Crystal structure of DNPEP, ZnMg form · the same entry in another collection · chain A against A, TM-score 1.00
Q2HJH1 · AlphaFold monomer V2.0 prediction for aspartyl aminopeptidase (Q2HJH1) · a predicted model of the same protein · chain A against A, TM-score 1.00

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 Q2HJH1
Elsewhere: RCSB PDB 3VAT · PDBe 3VAT · UniProt Q2HJH1

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