MolNFT v1 · #51970 · protein

Glycoside hydrolase family 15 glucoamylase from hypocrea jecorina

2VN4: “Glycoside hydrolase family 15 glucoamylase from hypocrea jecorina”. X-ray diffraction, 2 ligands (MAN, NAG), 4 pockets (best druggability 0.67). MolNFT v1 #51970 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 2VN4
Type: protein
Length: 599 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Glucoamylase
EC: 3.2.1.3
Ligands: MAN, NAG
Pockets: 4 · best druggability 0.67

Structure

x-ray diffraction · 1 distinct chain · 40% helix, 15% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Glucoamylase (EC 3.2.1.3)	protein	599	40% helix, 15% strand	—

Ligands and binding sites

MAN · alpha-D-mannopyranose · sugar · 8 copies · chains A
NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 3 copies · chains A
BTB · 2-[bis-(2-hydroxy-ethyl)-amino]-2-hydroxymethyl-propane-1,3-diol · additive · 2 copies · chains A

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

Pockets

4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	175	0.67	0.86	38	empty
2	181	0.59	0.81	32	BTB
3	70	0.32	0.75	20	empty
4	51	0.29	0.76	17	empty

Modifications

Observed in the structure: 10 glycan, 4 disulfide (O-glycosylation, disulfide, N-glycosylation).

Compared structures

2VN4 · Glycoside Hydrolase Family 15 Glucoamylase from Hypocrea jecorina · the same entry in another collection · 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
Elsewhere: RCSB PDB 2VN4 · PDBe 2VN4

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