MolNFT v1 · #141377 · protein

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

5Z5H · Beta-xylosidase: “Crystal structure of a thermostable glycoside hydrolase family 43 {beta}-1,4-xylosidase from geobacillus…”. X-ray diffraction, 2 ligands (XYS, CA), 5 pockets (best druggability 0.58). MolNFT v1 #141377 on…

PDB: 5Z5H
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: XYS, CA
Pockets: 5 · best druggability 0.58

Structure

x-ray diffraction · 1 distinct chain · 3% helix, 49% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Beta-xylosidase (EC 3.2.1.37)	protein	504	3% helix, 49% strand	Q2I2N4

Ligands and binding sites

XYS · alpha-D-xylopyranose · sugar · 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	280	0.58	0.78	21	empty
2	213	0.56	0.79	32	XYS
3	168	0.47	0.76	22	empty
4	165	0.47	0.76	29	empty
5	51	0.37	0.81	14	empty

Compared structures

5Z5H · 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

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 Q2I2N4
Elsewhere: RCSB PDB 5Z5H · PDBe 5Z5H · UniProt Q2I2N4

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