MolNFT v1 · #80687 · protein

From soil to structure: a novel dimeric family 3-beta-glucosidase isolated from compost using metagenomic analysis

3U4A · JMB19063: “From soil to structure: a novel dimeric family 3-beta-glucosidase isolated from compost using metagenomic…”. X-ray diffraction, 2 ligands (BGC, CA), 13 pockets (best druggability 0.85). MolNFT v1 #80687 on GenesisL1: 3D…

PDB: 3U4A
Type: protein
Length: 1,481 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: JMB19063
Ligands: BGC, CA
Pockets: 13 · best druggability 0.85

Structure

x-ray diffraction · 2 distinct chains · 34% helix, 19% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	JMB19063	protein	739	34% helix, 19% strand	—
B	JMB19063	protein	742	35% helix, 19% strand	—

Ligands and binding sites

BGC · beta-D-glucopyranose · sugar · 6 copies · chains A, B
CA · Calcium ion · metal · chains A

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

Pockets

13 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	279	0.85	0.96	36	empty
2	376	0.69	0.82	41	empty
3	348	0.68	0.81	37	empty
4	371	0.68	0.81	40	empty
5	341	0.67	0.81	35	empty

Interfaces

1 interface between chains.

A–B · 3422 Å² buried · 79 hydrogen bonds · protein-protein

Compared structures

3U4A · From soil to structure: a novel dimeric family 3-beta-glucosidase isolated from compost… · 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 3U4A · PDBe 3U4A

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