MolNFT v1 · #82257 · protein

Crystal structure of saccharomyces cerevisiae ATG7 (1-613)

3VH2 · Ubiquitin-like modifier-activating enzyme ATG7: “Crystal structure of saccharomyces cerevisiae ATG7 (1-613)”. X-ray diffraction, 1 ligand (ZN), 5 pockets (best druggability 0.59). MolNFT v1 #82257 on GenesisL1: 3D structure, binding…

PDB: 3VH2
Type: protein
Length: 582 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Ubiquitin-like modifier-activating enzyme ATG7
UniProt: P38862
Ligands: ZN
Pockets: 5 · best druggability 0.59

Structure

x-ray diffraction · 1 distinct chain · 33% helix, 25% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Ubiquitin-like modifier-activating enzyme ATG7	protein	582	33% helix, 25% strand	P38862

Ligands and binding sites

ZN · Zinc ion · metal · 2 copies · chains A

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	242	0.59	0.80	41	empty
2	138	0.47	0.77	25	empty
3	111	0.40	0.76	23	empty
4	105	0.39	0.76	28	empty
5	60	0.29	0.74	12	empty

Compared structures

3VH2 · Crystal structure of Saccharomyces cerevisiae Atg7 (1-613) · the same entry in another collection · chain A against A, TM-score 1.00
P38862 · AlphaFold monomer V2.0 prediction for ubiquitin-like modifier- activating enzyme ATG7… · a predicted model of the same protein · chain A against A, TM-score 0.55

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 P38862
Elsewhere: RCSB PDB 3VH2 · PDBe 3VH2 · UniProt P38862

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