MolNFT v1 · #103759 · protein

Crystal structure of a beta-1,3-glucanase from mycobacterium marinum

4PQ9: “Crystal structure of a beta-1,3-glucanase from mycobacterium marinum”. X-ray diffraction, 1 ligand (MG), 3 pockets (best druggability 0.70). MolNFT v1 #103759 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 4PQ9
Type: protein
Length: 466 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Beta-1,3-glucanase
UniProt: B2HE62
Ligands: MG
Pockets: 3 · best druggability 0.70

Structure

x-ray diffraction · 1 distinct chain · 3% helix, 42% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Beta-1,3-glucanase	protein	233	3% helix, 42% strand	B2HE62

Ligands and binding sites

MG · Magnesium ion · metal · 3 copies · chains A, B
BTB · 2-[bis-(2-hydroxy-ethyl)-amino]-2-hydroxymethyl-propane-1,3-diol · additive · 2 copies · chains A, B
EDO · 1,2-ethanediol · additive · 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, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	687	0.70	0.78	70	BTB, EDO
2	314	0.56	0.76	39	BTB
3	74	0.32	0.75	14	empty

Interfaces

1 interface between chains.

A–B · 617 Å² buried · 6 hydrogen bonds · protein-protein

Compared structures

4PQ9 · Crystal Structure of a Beta-1,3-glucanase from Mycobacterium marinum · 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
Every structure of UniProt B2HE62
Elsewhere: RCSB PDB 4PQ9 · PDBe 4PQ9 · UniProt B2HE62

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