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Glycoside hydrolase ligand structure 1

Analyse Glycoside hydrolase ligand structure 1 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5E97
Type: protein
Length: 459 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Heparanase
EC: 3.2.1.166
UniProt: Q9Y251
Ligands: NPO, NAG, BDP, NDG, CL
Pockets: 5 · best druggability 0.55

Structure

x-ray diffraction · 2 distinct chains · 32% helix, 28% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Heparanase (EC 3.2.1.166)	protein	385	32% helix, 27% strand	Q9Y251
B	Heparanase (EC 3.2.1.166)	protein	74	34% helix, 32% strand	Q9Y251

Ligands and binding sites

NPO · P-nitrophenol · ligand · chains A, B
NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains A, B
BDP · beta-D-glucopyranuronic acid · sugar · 2 copies · chains A, B
NDG · 2-acetamido-2-deoxy-alpha-D-glucopyranose · sugar · 2 copies · chains A, B
CL · Chloride ion · ion · 4 copies · chains A, B

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

Pockets

5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	289	0.55	0.76	37	BDP, NDG, CL, NPO
2	107	0.50	0.81	22	empty
3	79	0.48	0.83	23	empty
4	61	0.35	0.77	14	empty
5	55	0.26	0.73	18	empty

Interfaces

1 interface between chains.

A–B · 4309 Å² buried · 63 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 4 glycan, 1 disulfide (N-glycosylation, disulfide).

Compared structures

5E97 · Glycoside Hydrolase ligand structure 1 · the same entry in another collection · chain A against A, TM-score 1.00
Q9Y251 · AlphaFold monomer V2.0 prediction for heparanase (Q9Y251) · a predicted model of the same protein · chain A 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 Q9Y251
Elsewhere: RCSB PDB 5E97 · PDBe 5E97 · UniProt Q9Y251

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