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Structure of a family 31 alpha glycosidase

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

PDB: 1XSJ
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
Pockets: 20 · best druggability 0.82

Structure

x-ray diffraction · 1 distinct chain · 21% helix, 34% 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	21% helix, 34% strand	P31434

Ligands and binding sites

TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · 12 copies · chains A, B, D, E, C, F

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	184	0.82	0.96	45	empty
2	187	0.81	0.96	47	empty
3	181	0.81	0.96	44	empty
4	855	0.74	0.78	95	TRS
5	953	0.74	0.77	114	TRS

Interfaces

9 interfaces between chains.

A–D · 2122 Å² buried · 15 hydrogen bonds · protein-protein
B–C · 2105 Å² buried · 15 hydrogen bonds · protein-protein
E–F · 2098 Å² buried · 18 hydrogen bonds · protein-protein
D–E · 1047 Å² buried · 13 hydrogen bonds · protein-protein
A–B · 1046 Å² buried · 13 hydrogen bonds · protein-protein

Compared structures

1XSJ · Structure of a Family 31 alpha glycosidase · the same entry in another collection · chain D against D, 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 1XSJ · PDBe 1XSJ · UniProt P31434

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