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Crystal structure of GH31 alpha-xylosidase from a soil metagenome complexed with xylose

Analyse Crystal structure of GH31 alpha-xylosidase from a soil metagenome complexed… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5ZN7
Type: protein
Length: 5,421 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Alpha-xylosidase MEXYL31
Ligands: XYS
Pockets: 20 · best druggability 0.88

Structure

x-ray diffraction · 5 distinct chains · 25% helix, 30% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, D	Alpha-xylosidase MEXYL31	protein	680	25% helix, 31% strand	—
B	Alpha-xylosidase MEXYL31	protein	682	25% helix, 30% strand	—
C, H	Alpha-xylosidase MEXYL31	protein	676	25% helix, 30% strand	—
E, F	Alpha-xylosidase MEXYL31	protein	675	25% helix, 31% strand	—
G	Alpha-xylosidase MEXYL31	protein	677	25% helix, 30% strand	—

Ligands and binding sites

XYS · alpha-D-xylopyranose · sugar · 5 copies · chains A, C, D, F, 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	909	0.88	0.90	120	empty
2	887	0.88	0.90	113	empty
3	684	0.86	0.90	88	empty
4	754	0.86	0.89	86	empty
5	400	0.81	0.89	51	empty

Interfaces

12 interfaces between chains.

E–F · 1539 Å² buried · 23 hydrogen bonds · protein-protein
A–C · 1530 Å² buried · 22 hydrogen bonds · protein-protein
D–H · 1527 Å² buried · 20 hydrogen bonds · protein-protein
B–G · 1525 Å² buried · 22 hydrogen bonds · protein-protein
E–H · 1406 Å² buried · 20 hydrogen bonds · protein-protein

Compared structures

5ZN7 · Crystal structure of GH31 alpha-xylosidase from a soil metagenome complexed with xylose · 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
Elsewhere: RCSB PDB 5ZN7 · PDBe 5ZN7

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