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Escherichia COLI K12 ygjk complexed with glucose

Analyse Escherichia COLI K12 ygjk complexed with glucose in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3W7S
Type: protein
Length: 1,520 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Uncharacterized protein ygjk
UniProt: P42592
Ligands: GLC, CA
Pockets: 10 · best druggability 0.78

Structure

x-ray diffraction · 1 distinct chain · 34% helix, 24% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Uncharacterized protein ygjk	protein	760	34% helix, 24% strand	P42592

Ligands and binding sites

GLC · alpha-D-glucopyranose · sugar · 11 copies · chains A, B
CA · Calcium ion · metal · 2 copies · chains A, 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, 4 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1120	0.78	0.80	93	GLC
2	846	0.76	0.79	81	GLC
3	283	0.65	0.81	28	empty
4	498	0.65	0.77	42	empty
5	99	0.39	0.76	19	empty

Interfaces

1 interface between chains.

A–B · 888 Å² buried · 12 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 2 disulfide (disulfide).

Compared structures

3W7S · Escherichia coli K12 YgjK complexed with glucose · the same entry in another collection · chain A against A, TM-score 1.00
P42592 · AlphaFold monomer V2.0 prediction for glucosidase ygjk (P42592) · 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 P42592
Elsewhere: RCSB PDB 3W7S · PDBe 3W7S · UniProt P42592

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