MolNFT v1 · #26072 · protein

Crystal structure of alpha-xylosidase from escherichia COLI

1WE5 · Putative family 31 glucosidase yici: “Crystal structure of alpha-xylosidase from escherichia COLI”. X-ray diffraction, 20 pockets (best druggability 0.80). MolNFT v1 #26072 on GenesisL1: 3D structure, binding sites and pockets in…

PDB: 1WE5
Type: protein
Length: 4,557 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 0.80

Structure

x-ray diffraction · 6 distinct chains · 21% helix, 33% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Putative family 31 glucosidase yici (EC 3.2.1.-)	protein	772	22% helix, 34% strand	P31434
B	Putative family 31 glucosidase yici (EC 3.2.1.-)	protein	760	21% helix, 33% strand	P31434
C	Putative family 31 glucosidase yici (EC 3.2.1.-)	protein	756	21% helix, 33% strand	P31434
D	Putative family 31 glucosidase yici (EC 3.2.1.-)	protein	757	22% helix, 33% strand	P31434
E	Putative family 31 glucosidase yici (EC 3.2.1.-)	protein	755	21% helix, 33% strand	P31434
F	Putative family 31 glucosidase yici (EC 3.2.1.-)	protein	757	22% helix, 34% strand	P31434

Ligands and binding sites

MES · 2-(N-morpholino)-ethanesulfonic acid · additive · 6 copies · chains A, B, C, D, E, 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	164	0.80	0.96	47	empty
2	159	0.80	0.96	45	empty
3	931	0.78	0.80	98	MES
4	402	0.75	0.85	52	MES
5	88	0.73	0.96	23	empty

Interfaces

11 interfaces between chains.

C–F · 2062 Å² buried · 17 hydrogen bonds · protein-protein
B–E · 2051 Å² buried · 24 hydrogen bonds · protein-protein
A–D · 2013 Å² buried · 14 hydrogen bonds · protein-protein
B–D · 1045 Å² buried · 15 hydrogen bonds · protein-protein
D–F · 1039 Å² buried · 11 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 114 modified (engineered).

Compared structures

1WE5 · Crystal Structure of Alpha-Xylosidase from Escherichia coli · the same entry in another collection · chain F against F, TM-score 1.00
P31434 · AlphaFold monomer V2.0 prediction for alpha-xylosidase (P31434) · a predicted model of the same protein · chain C 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 1WE5 · PDBe 1WE5 · UniProt P31434

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