Research workbench
Crystal structure of the complex of human alpha-thrombin and non- hydrolyzable bifunctional inhibitors, hirutonin-2 and hirutonin-6
Analyse Crystal structure of the complex of human alpha-thrombin and non- hydrolyzable… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1IHS
- Type
- protein
- Length
- 306 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
- EC
- 3.4.21.5
- UniProt
- P00734, P28504
- Ligands
- ACE
- Pockets
- 2 · best druggability 0.69
Structure
x-ray diffraction · 3 distinct chains · 17% helix, 29% 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 | protein | 19 | 16% helix, 5% strand | P28504 |
Ligands and binding sites
- ACE · Acetyl group · ligand · chains H, I
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 | 58 | 0.69 | 0.97 | 22 | empty |
| 2 | 55 | 0.29 | 0.75 | 17 | empty |
Interfaces
2 interfaces between chains.
- H–I · 1356 Ų buried · 23 hydrogen bonds · protein-protein
- L–H · 1106 Ų buried · 24 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide, 1 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 1IHS · PDBe 1IHS · UniProt P00734 · UniProt P28504
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