Research workbench
X-ray structure of the human alpha-thrombin complex with a tripeptide phosphonate inhibitor.
Analyse X-ray structure of the human alpha-thrombin complex with a tripeptide… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1H8D
- Type
- protein
- Length
- 289 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
- PHW
- Pockets
- 2 · best druggability 0.54
Structure
x-ray diffraction · 3 distinct chains · 18% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| H | Thrombin (EC 3.4.21.5) | protein | 251 | 16% helix, 36% strand | P00734 |
| I | Hirudin I | protein | 10 | 30% helix, 0% strand | P01050 |
| L | Thrombin (EC 3.4.21.5) | protein | 28 | 36% helix, 0% strand | P00734 |
Ligands and binding sites
- PHW · N-[(benzyloxy)carbonyl]-beta-phenyl-D-phenylalanyl-N-{(1S,3E)-1-[dihydroxy(diphenoxy)-lambda~5~-phosphanyl]-4-methoxybut-3-en-1-yl}-L-prolinamide · ligand · 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 | 276 | 0.54 | 0.76 | 42 | PHW |
| 2 | 56 | 0.28 | 0.74 | 11 | empty |
Interfaces
2 interfaces between chains.
- H–L · 1119 Ų buried · 28 hydrogen bonds · protein-protein
- H–I · 629 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide, 1 modified (disulfide, sulfation).
Compared structures
- 1H8D · X-ray structure of the human alpha-thrombin complex with a tripeptide phosphonate… · 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 0.54
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 1H8D · PDBe 1H8D · UniProt P00734 · UniProt P01050
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