Research workbench
Crystal structure of human proheparanase, in complex with glucuronic acid configured aziridine probe JJB355
Analyse Crystal structure of human proheparanase, in complex with glucuronic acid… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5LA7
- 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
- 6S6, NAG, FUC
- Pockets
- 4 · best druggability 0.67
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
- 6S6 · (1~{S},2~{R},3~{S},4~{S},5~{S},6~{R})-2-(8-azidooctylamino)-3,4,5,6-tetrakis(oxidanyl) cyclohexane-1-carboxylic acid · ligand · chains A
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 5 copies · chains A
- FUC · alpha-L-fucopyranose · sugar · chains A
- EDO · 1,2-ethanediol · additive · 6 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.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 322 | 0.67 | 0.81 | 34 | 6S6 |
| 2 | 89 | 0.45 | 0.80 | 22 | EDO |
| 3 | 79 | 0.36 | 0.76 | 14 | empty |
| 4 | 89 | 0.33 | 0.74 | 19 | empty |
Modifications
Observed in the structure: 4 glycan, 2 disulfide, 1 covalent (N-glycosylation, disulfide, covalent ligand).
Compared structures
- 5LA7 · Crystal structure of human proheparanase, in complex with glucuronic acid configured… · 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 5LA7 · PDBe 5LA7 · UniProt Q9Y251
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