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Structure of a family 31 alpha glycosidase glycosyl-enzyme intermediate

Analyse Structure of a family 31 alpha glycosidase glycosyl-enzyme intermediate in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 1XSK
Type: protein
Length: 4,638 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Putative family 31 glucosidase yici
EC: 3.2.1.-
UniProt: P31434
Ligands: XYF, SO4
Pockets: 20 · best druggability 0.85

Structure

x-ray diffraction · 1 distinct chain · 22% helix, 33% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D, E, F	Putative family 31 glucosidase yici (EC 3.2.1.-)	protein	773	22% helix, 33% strand	P31434

Ligands and binding sites

XYF · 5(R)-fluoro-beta-D-xylopyranose · ligand · 4 copies · chains A, B, C, E
SO4 · Sulfate ion · ion · 13 copies · chains A, B, C, D, E, F
MPO · 3[N-morpholino]propane sulfonic acid · additive · 4 copies · chains B, C, D, E

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	303	0.85	0.95	66	empty
2	129	0.79	0.97	33	empty
3	119	0.75	0.95	29	empty
4	84	0.72	0.95	26	empty
5	92	0.71	0.94	25	empty

Interfaces

9 interfaces between chains.

E–F · 2057 Å² buried · 16 hydrogen bonds · protein-protein
B–C · 2042 Å² buried · 12 hydrogen bonds · protein-protein
A–D · 2017 Å² buried · 14 hydrogen bonds · protein-protein
A–F · 1020 Å² buried · 12 hydrogen bonds · protein-protein
A–B · 1019 Å² buried · 14 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 4 covalent (covalent ligand).

Compared structures

1XSK · Structure of a Family 31 alpha glycosidase glycosyl-enzyme intermediate · the same entry in another collection · chain B against B, TM-score 1.00
P31434 · AlphaFold monomer V2.0 prediction for alpha-xylosidase (P31434) · a predicted model of the same protein · chain A against A, TM-score 0.99

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 P31434
Elsewhere: RCSB PDB 1XSK · PDBe 1XSK · UniProt P31434

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