MolNFT v1 · #67536 · protein
Crystal structure of heparin lyase I complexed with disaccharide heparin
3IN9: “Crystal structure of heparin lyase I complexed with disaccharide heparin”. X-ray diffraction, 3 ligands (UAP, SGN, CA), 3 pockets (best druggability 0.70). MolNFT v1 #67536 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 3IN9
- Type
- protein
- Length
- 373 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Heparin lyase I
- Ligands
- UAP, SGN, CA
- Pockets
- 3 · best druggability 0.70
Structure
x-ray diffraction · 1 distinct chain · 10% helix, 47% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Heparin lyase I | protein | 373 | 10% helix, 47% strand | — |
Ligands and binding sites
- UAP · 4-deoxy-2-O-sulfo-alpha-L-threo-hex-4-enopyranuronic acid · ligand · 2 copies · chains A
- SGN · 2-deoxy-6-O-sulfo-2-(sulfoamino)-alpha-D-glucopyranose · sugar · 2 copies · chains A
- CA · Calcium ion · metal · 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.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 677 | 0.70 | 0.78 | 61 | SGN, UAP |
| 2 | 97 | 0.48 | 0.81 | 22 | empty |
| 3 | 91 | 0.42 | 0.78 | 16 | empty |
Compared structures
- 3IN9 · Crystal structure of heparin lyase I complexed with disaccharide heparin · the same entry in another collection · 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
- Elsewhere: RCSB PDB 3IN9 · PDBe 3IN9
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