MolNFT v1 · #4839 · protein
Plasma beta antithrombin-III
1E04: “Plasma beta antithrombin-III”. X-ray diffraction, 4 ligands (NAG, MAN, BMA), 7 pockets (best druggability 0.76). MolNFT v1 #4839 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 1E04
- Type
- protein
- Length
- 815 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Antithrombin-III
- UniProt
- P01008
- Ligands
- NAG, MAN, BMA, PO4
- Pockets
- 7 · best druggability 0.76
Structure
x-ray diffraction · 2 distinct chains · 30% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| I | Antithrombin-III | protein | 403 | 30% helix, 32% strand | P01008 |
| L | Antithrombin-III | protein | 412 | 29% helix, 33% strand | P01008 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 12 copies · chains I, L
- MAN · alpha-D-mannopyranose · sugar · 3 copies
- BMA · beta-D-mannopyranose · sugar · 2 copies
- PO4 · Phosphate ion · ion · chains L
- GOL · Glycerol · additive · 2 copies · chains I, L
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 555 | 0.76 | 0.83 | 55 | empty |
| 2 | 123 | 0.67 | 0.89 | 20 | GOL |
| 3 | 133 | 0.67 | 0.88 | 20 | GOL |
| 4 | 205 | 0.53 | 0.78 | 29 | empty |
| 5 | 108 | 0.38 | 0.75 | 20 | empty |
Interfaces
1 interface between chains.
- I–L · 938 Ų buried · 17 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide, 6 glycan (disulfide, N-glycosylation).
Compared structures
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 P01008
- Elsewhere: RCSB PDB 1E04 · PDBe 1E04 · UniProt P01008
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