Research workbench
Thrombin complexed with hirugen and a beta-strand mimetic inhibitor
Analyse Thrombin complexed with hirugen and a beta-strand mimetic inhibitor in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1A46
- Type
- protein
- Length
- 286 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Alpha-thrombin (small subunit); Alpha-thrombin (large subunit); Hirugen
- EC
- 3.4.21.5
- UniProt
- P00734, P09945
- Ligands
- 00K, NA
- Pockets
- 2 · best druggability 0.52
Structure
x-ray diffraction · 3 distinct chains · 15% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| L | Alpha-thrombin (small subunit) (EC 3.4.21.5) | protein | 26 | 38% helix, 0% strand | P00734 |
| H | Alpha-thrombin (large subunit) (EC 3.4.21.5) | protein | 250 | 14% helix, 38% strand | P00734 |
| I | Hirugen | protein | 10 | 0% helix, 0% strand | P09945 |
Ligands and binding sites
- 00K · (1S,7S)-7-amino-N-[(2R,3S)-7-amino-1-(cyclohexylamino)-2-hydroxy-1-oxoheptan-3-yl]-7-benzyl-8-oxohexahydro-1H-pyrazolo[1,2-a]pyridazine-1-carboxamide · ligand · chains H
- NA · Sodium ion · metal · 2 copies · chains H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 206 | 0.52 | 0.77 | 38 | 00K |
| 2 | 79 | 0.38 | 0.77 | 15 | empty |
Interfaces
2 interfaces between chains.
- L–H · 1077 Ų buried · 22 hydrogen bonds · protein-protein
- H–I · 627 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide, 1 covalent, 1 modified (disulfide, covalent ligand, sulfation).
Compared structures
- 1A46 · Thrombin complexed with hirugen and a beta-strand mimetic inhibitor · the same entry in another collection · chain L against L, TM-score 1.00
- P00734 · AlphaFold monomer V2.0 prediction for prothrombin (P00734) · a predicted model of the same protein · chain H against A, TM-score 0.92
- P09945 · AlphaFold monomer V2.0 prediction for hirudin variant-2 (P09945) · a predicted model of the same protein · chain I against A, TM-score 0.53
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 P00734
- Every structure of UniProt P09945
- Elsewhere: RCSB PDB 1A46 · PDBe 1A46 · UniProt P00734 · UniProt P09945
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