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Crystal structure of apo human proheparanase

Analyse Crystal structure of apo human proheparanase in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5LA4
Type: protein
Length: 508 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Heparanase
EC: 3.2.1.166
UniProt: Q9Y251
Ligands: NAG, BMA, FUC
Pockets: 4 · best druggability 0.62

Structure

x-ray diffraction · 1 distinct chain · 37% helix, 25% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Heparanase (EC 3.2.1.166)	protein	508	37% helix, 25% strand	Q9Y251

Ligands and binding sites

NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 5 copies · chains A
BMA · beta-D-mannopyranose · sugar
FUC · alpha-L-fucopyranose · sugar · chains A
EDO · 1,2-ethanediol · additive · 5 copies · chains A

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

Pockets

4 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	240	0.62	0.81	37	EDO
2	88	0.46	0.81	24	EDO
3	67	0.36	0.77	14	empty
4	100	0.36	0.74	21	empty

Modifications

Observed in the structure: 4 glycan, 2 disulfide (N-glycosylation, disulfide).

Compared structures

5LA4 · Crystal structure of apo human proheparanase · 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 5LA4 · PDBe 5LA4 · UniProt Q9Y251

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