Research workbench
X-ray crystal structure of human alpha-thrombin with a tripeptide phosphonate inhibitor.
Analyse X-ray crystal structure of human alpha-thrombin with a tripeptide phosphonate… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1H8I
- Type
- protein
- Length
- 290 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Thrombin; Hirudin I
- EC
- 3.4.21.5
- UniProt
- P00734, P01050
- Ligands
- PHV
- Pockets
- 4 · best druggability 0.56
Structure
x-ray diffraction · 3 distinct chains · 18% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| H | Thrombin (EC 3.4.21.5) | protein | 253 | 15% helix, 35% strand | P00734 |
| I | Hirudin I | protein | 10 | 30% helix, 0% strand | P01050 |
| L | Thrombin (EC 3.4.21.5) | protein | 27 | 37% helix, 0% strand | P00734 |
Ligands and binding sites
- PHV · N-[(benzyloxy)carbonyl]-beta-phenyl-D-phenylalanyl-N-[(1S)-4-methoxy-1-phosphonobutyl]-L-prolinamide · ligand · chains H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 289 | 0.56 | 0.76 | 42 | PHV |
| 2 | 70 | 0.38 | 0.78 | 17 | empty |
| 3 | 54 | 0.31 | 0.76 | 12 | empty |
| 4 | 52 | 0.26 | 0.73 | 17 | empty |
Interfaces
2 interfaces between chains.
- H–L · 1105 Ų buried · 29 hydrogen bonds · protein-protein
- H–I · 646 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide, 1 covalent, 1 modified (disulfide, covalent ligand, sulfation).
Compared structures
- 1H8I · X-ray crystal structure of human alpha-thrombin with a tripeptide phosphonate inhibitor. · the same entry in another collection · chain H against H, TM-score 1.00
- P01050 · AlphaFold monomer V2.0 prediction for hirudin variant-1 (P01050) · a predicted model of the same protein · chain I against A, TM-score 0.62
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 P01050
- Elsewhere: RCSB PDB 1H8I · PDBe 1H8I · UniProt P00734 · UniProt P01050
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