MolNFT v1 · #31221 · protein
The 2.6 a structure of antithrombin indicates a conformational change at the heparin binding site
2ANT: “The 2.6 a structure of antithrombin indicates a conformational change at the heparin binding site”. X-ray diffraction, 1 ligand (NAA), 9 pockets (best druggability 0.67). MolNFT v1 #31221 on GenesisL1: 3D structure, binding sites…
- PDB
- 2ANT
- Type
- protein
- Length
- 817 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Antithrombin
- UniProt
- P01008
- Ligands
- NAA
- Pockets
- 9 · best druggability 0.67
Structure
x-ray diffraction · 2 distinct chains · 29% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| L | Antithrombin | protein | 398 | 30% helix, 31% strand | P01008 |
| I | Antithrombin | protein | 419 | 28% helix, 27% strand | P01008 |
Ligands and binding sites
- NAA · 2-acetamido-2-deoxy-beta-D-allopyranose · sugar · 2 copies · chains L, I
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 93 | 0.67 | 0.91 | 18 | empty |
| 2 | 61 | 0.65 | 0.94 | 26 | empty |
| 3 | 96 | 0.65 | 0.89 | 19 | empty |
| 4 | 464 | 0.61 | 0.75 | 67 | empty |
| 5 | 256 | 0.56 | 0.77 | 34 | empty |
Interfaces
1 interface between chains.
- L–I · 419 Ų buried · 14 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide, 2 glycan (disulfide, N-glycosylation).
Compared structures
- 2ANT · The 2.6 a structure of antithrombin indicates a conformational change at the heparin… · the same entry in another collection · chain L against L, TM-score 1.00
- P01008 · AlphaFold monomer V2.0 prediction for antithrombin-III (P01008) · a predicted model of the same protein · chain I against A, TM-score 0.90
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 2ANT · PDBe 2ANT · UniProt P01008
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