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Glycoside hydrolase family 8 xylanase

Analyse Glycoside hydrolase family 8 xylanase in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5YXT
Type: protein
Length: 1,516 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Reducing end xylose-releasing exo-oligoxylanase
UniProt: R9L536
Pockets: 11 · best druggability 0.83

Structure

x-ray diffraction · 1 distinct chain · 52% helix, 8% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D	Reducing end xylose-releasing exo-oligoxylanase	protein	379	52% helix, 8% strand	R9L536

Pockets

11 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	1147	0.83	0.84	103	empty
2	266	0.57	0.78	32	empty
3	194	0.56	0.80	30	empty
4	242	0.56	0.78	33	empty
5	243	0.55	0.77	45	empty

Interfaces

5 interfaces between chains.

A–D · 560 Å² buried · 2 hydrogen bonds · protein-protein
A–C · 477 Å² buried · 2 hydrogen bonds · protein-protein
B–C · 441 Å² buried · 4 hydrogen bonds · protein-protein
C–D · 225 Å² buried · 1 hydrogen bond · protein-protein
A–B · 179 Å² buried · 0 hydrogen bonds · protein-protein

Compared structures

5YXT · Crystal structure of reducing end xylose-releasing exo-oligoxylanase · 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 R9L536
Elsewhere: RCSB PDB 5YXT · PDBe 5YXT · UniProt R9L536

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