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A bacterial protein structure in glycoside hydrolase family 31

Analyse A bacterial protein structure in glycoside hydrolase family 31 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5AEE
Type: protein
Length: 1,335 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v2 / PDB Bank
Contract: 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
Owner: 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
Resolution: 1.85
Source: ESCHERICHIA COLI
Molecule: Alpha-glucosidase yihq
EC: 3.2.1.20
UniProt: P32138
Ligands: NSQ, CA, CL
Pockets: 10 · best druggability 0.83

Structure

x-ray diffraction · resolution 1.85 · 2 distinct chains · 27% helix, 30% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Alpha-glucosidase yihq (EC 3.2.1.20)	protein	667	27% helix, 30% strand	P32138
B	Alpha-glucosidase yihq (EC 3.2.1.20)	protein	668	26% helix, 30% strand	P32138

Ligands and binding sites

NSQ · 4-nitrophenyl alpha-D-6-sulfoquinovoside · sugar · 2 copies · chains A, B
CA · Calcium ion · metal · 3 copies · chains A, B
CL · Chloride ion · ion · chains B
MPD · (4S)-2-methyl-2,4-pentanediol · additive · chains B

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

10 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	256	0.83	0.95	38	NSQ
2	271	0.80	0.92	41	NSQ, CL
3	828	0.70	0.76	88	empty
4	80	0.43	0.80	24	empty
5	108	0.41	0.76	25	empty

Interfaces

1 interface between chains.

A–B · 821 Å² buried · 22 hydrogen bonds · protein-protein

Compared structures

5AEE · A bacterial protein structure in glycoside hydrolase family 31 · the same entry in another collection · chain A against A, TM-score 1.00
P32138 · AlphaFold monomer V2.0 prediction for sulfoquinovosidase (P32138) · a predicted model of the same protein · chain B 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 P32138
Elsewhere: RCSB PDB 5AEE · PDBe 5AEE · UniProt P32138

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