MolNFT v1 · #10141 · protein
Crystal structure of the complex of human alpha-thrombin and non- hydrolyzable bifunctional inhibitors, hirutonin-2 and hirutonin-6
1IHT · Alpha-thrombin (small subunit): “Crystal structure of the complex of human alpha-thrombin and non- hydrolyzable bifunctional inhibitors…”. X-ray diffraction, 2 ligands (FBE, ACE), 1 pocket (best druggability 0.27). MolNFT v1 #10141…
- PDB
- 1IHT
- Type
- protein
- Length
- 296 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Alpha-thrombin (small subunit); Alpha-thrombin (large subunit); Hirutonin-6
- EC
- 3.4.21.5
- UniProt
- P00734, P28504
- Ligands
- FBE, ACE
- Pockets
- 1 · best druggability 0.27
Structure
x-ray diffraction · 3 distinct chains · 16% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| L | Alpha-thrombin (small subunit) (EC 3.4.21.5) | protein | 29 | 34% helix, 0% strand | P00734 |
| H | Alpha-thrombin (large subunit) (EC 3.4.21.5) | protein | 258 | 15% helix, 34% strand | P00734 |
| I | Hirutonin-6 | protein | 9 | 0% helix, 11% strand | P28504 |
Ligands and binding sites
- FBE · (3E)-5-aminopent-3-enoic acid · ligand · 2 copies · chains H, I
- ACE · Acetyl group · ligand · chains H, I
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 59 | 0.27 | 0.73 | 13 | empty |
Interfaces
2 interfaces between chains.
- L–H · 1156 Ų buried · 24 hydrogen bonds · protein-protein
- H–I · 972 Ų buried · 17 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide, 3 covalent, 1 d-amino, 1 modified (disulfide, covalent ligand, D-amino acid, nonstandard).
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 P00734
- Every structure of UniProt P28504
- Elsewhere: RCSB PDB 1IHT · PDBe 1IHT · UniProt P00734 · UniProt P28504
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