MolNFT v1 · #54211 · protein

Crystal structure of E.COLI bgla

2XHY · 6-phospho-beta-glucosidase bgla: “Crystal structure of E.COLI bgla”. X-ray diffraction, 2 ligands (BR, SO4), 12 pockets (best druggability 0.82). MolNFT v1 #54211 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 2XHY
Type: protein
Length: 1,868 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: 6-phospho-beta-glucosidase bgla
EC: 3.2.1.86
UniProt: Q46829
Ligands: BR, SO4
Pockets: 12 · best druggability 0.82

Structure

x-ray diffraction · 4 distinct chains · 42% helix, 15% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	6-phospho-beta-glucosidase bgla (EC 3.2.1.86)	protein	470	41% helix, 15% strand	Q46829
B	6-phospho-beta-glucosidase bgla (EC 3.2.1.86)	protein	468	42% helix, 15% strand	Q46829
C	6-phospho-beta-glucosidase bgla (EC 3.2.1.86)	protein	466	40% helix, 15% strand	Q46829
D	6-phospho-beta-glucosidase bgla (EC 3.2.1.86)	protein	464	43% helix, 17% strand	Q46829

Ligands and binding sites

BR · Bromide ion · ion · 19 copies · chains A, B, C, D
SO4 · Sulfate ion · ion · 5 copies · chains A, B, C, D

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

Pockets

12 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	164	0.82	0.98	25	empty
2	171	0.82	0.97	26	empty
3	583	0.75	0.82	57	BR, SO4
4	669	0.74	0.80	65	BR, SO4
5	650	0.73	0.80	62	SO4

Interfaces

3 interfaces between chains.

A–B · 1870 Å² buried · 41 hydrogen bonds · protein-protein
C–D · 1869 Å² buried · 39 hydrogen bonds · protein-protein
A–D · 12 Å² buried · 0 hydrogen bonds · protein-protein

Compared structures

2XHY · Crystal Structure of E.coli BglA · the same entry in another collection · chain D against D, TM-score 1.00
Q46829 · AlphaFold monomer V2.0 prediction for 6-phospho-beta-glucosidase bgla (Q46829) · a predicted model of the same protein · chain D 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 Q46829
Elsewhere: RCSB PDB 2XHY · PDBe 2XHY · UniProt Q46829

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