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Crystal structure of a thermostable glycoside hydrolase family 43 {beta}-1,4-xylosidase from geobacillus thermoleovorans it-08 in complex with L-arabinose

Analyse Crystal structure of a thermostable glycoside hydrolase family 43… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5Z5F
Type: protein
Length: 504 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Beta-xylosidase
EC: 3.2.1.37
UniProt: Q2I2N4
Ligands: FUB, CA
Pockets: 5 · best druggability 0.59

Structure

x-ray diffraction · 1 distinct chain · 2% helix, 49% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Beta-xylosidase (EC 3.2.1.37)	protein	504	2% helix, 49% strand	Q2I2N4

Ligands and binding sites

FUB · beta-L-arabinofuranose · ligand · chains A
CA · Calcium ion · metal · chains A

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

Pockets

5 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	283	0.59	0.78	22	empty
2	222	0.55	0.78	35	FUB
3	176	0.48	0.76	28	empty
4	162	0.45	0.75	19	empty
5	58	0.38	0.80	15	empty

Compared structures

5Z5F · Crystal structure of a thermostable glycoside hydrolase family 43 {beta}-1,4-xylosidase… · the same entry in another collection · chain A against A, TM-score 1.00

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Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
Every structure of UniProt Q2I2N4
Elsewhere: RCSB PDB 5Z5F · PDBe 5Z5F · UniProt Q2I2N4

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