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Native crystal structure of a GH39 beta-xylosidase XYNB1 from geobacillus stearothermophilus

Analyse Native crystal structure of a GH39 beta-xylosidase XYNB1 from geobacillus… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 2BS9
Type: protein
Length: 4,008 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Beta-xylosidase
EC: 3.2.1.37
UniProt: Q9ZFM2
Ligands: CA
Pockets: 20 · best druggability 0.78

Structure

x-ray diffraction · 1 distinct chain · 32% helix, 26% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D, E, F, G, H	Beta-xylosidase (EC 3.2.1.37)	protein	501	32% helix, 26% strand	Q9ZFM2

Ligands and binding sites

CA · Calcium ion · metal · 7 copies · chains A, C, D, E, F, G, H

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

Pockets

20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	934	0.78	0.80	97	empty
2	609	0.77	0.83	46	empty
3	874	0.76	0.79	97	empty
4	665	0.76	0.81	44	empty
5	552	0.75	0.82	46	empty

Interfaces

15 interfaces between chains.

F–H · 2786 Å² buried · 55 hydrogen bonds · protein-protein
B–D · 2782 Å² buried · 59 hydrogen bonds · protein-protein
A–C · 2781 Å² buried · 59 hydrogen bonds · protein-protein
E–G · 2769 Å² buried · 62 hydrogen bonds · protein-protein
F–G · 1644 Å² buried · 27 hydrogen bonds · protein-protein

Compared structures

2BS9 · Native crystal structure of a GH39 beta-xylosidase XynB1 from Geobacillus… · the same entry in another collection · chain H against H, TM-score 1.00
Q9ZFM2 · AlphaFold monomer V2.0 prediction for beta-xylosidase (Q9ZFM2) · a predicted model of the same protein · 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 Q9ZFM2
Elsewhere: RCSB PDB 2BS9 · PDBe 2BS9 · UniProt Q9ZFM2

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