MolNFT v1 · #117476 · protein

Crystal structure of human heparanase in complex with hepmer M09S05A

5E9B: “Crystal structure of human heparanase in complex with hepmer M09S05A”. X-ray diffraction, 5 ligands (GNS, NAG, BDP), 3 pockets (best druggability 0.56). MolNFT v1 #117476 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5E9B
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: GNS, NAG, BDP, SGN, CL
Pockets: 3 · best druggability 0.56

Structure

x-ray diffraction · 2 distinct chains · 31% helix, 28% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Heparanase (EC 3.2.1.166)	protein	385	30% helix, 27% strand	Q9Y251
B	Heparanase (EC 3.2.1.166)	protein	74	34% helix, 32% strand	Q9Y251

Ligands and binding sites

GNS · 2-deoxy-2-(sulfoamino)-alpha-D-glucopyranose · ligand · chains A
NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 3 copies · chains A
BDP · beta-D-glucopyranuronic acid · sugar · 2 copies · chains A, B
SGN · 2-deoxy-6-O-sulfo-2-(sulfoamino)-alpha-D-glucopyranose · sugar · chains A, B
CL · Chloride ion · ion · chains A

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	301	0.56	0.76	35	BDP, SGN
2	64	0.46	0.83	20	CL
3	85	0.44	0.80	18	empty

Interfaces

1 interface between chains.

A–B · 4338 Å² buried · 67 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 3 glycan, 1 disulfide (N-glycosylation, disulfide).

Compared structures

5E9B · Crystal structure of human heparanase in complex with HepMer M09S05a · 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 5E9B · PDBe 5E9B · UniProt Q9Y251

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