MolNFT v1 · #9297 · protein
The structure of a complex of bovine alpha-thrombin and recombinant hirudin at 2.8 ångströms resolution
1HRT · Thrombin (small subunit): “The structure of a complex of bovine alpha-thrombin and recombinant hirudin at 2.8 ångströms resolution”. X-ray diffraction, 5 pockets (best druggability 0.69). MolNFT v1 #9297 on GenesisL1: 3D structure…
- PDB
- 1HRT
- Type
- protein
- Length
- 360 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Thrombin (small subunit); Thrombin (large subunit); Hirudin
- EC
- 3.4.21.5
- UniProt
- P00735, P01050
- Pockets
- 5 · best druggability 0.69
Structure
x-ray diffraction · 3 distinct chains · 8% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| L | Thrombin (small subunit) (EC 3.4.21.5) | protein | 36 | 19% helix, 0% strand | P00735 |
| H | Thrombin (large subunit) (EC 3.4.21.5) | protein | 259 | 8% helix, 34% strand | P00735 |
| I | Hirudin | protein | 65 | 0% helix, 23% strand | P01050 |
Pockets
5 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 67 | 0.69 | 0.95 | 16 | empty |
| 2 | 77 | 0.39 | 0.78 | 18 | empty |
| 3 | 64 | 0.34 | 0.77 | 14 | empty |
| 4 | 73 | 0.34 | 0.76 | 15 | empty |
| 5 | 60 | 0.31 | 0.76 | 17 | empty |
Interfaces
2 interfaces between chains.
- H–I · 1825 Ų buried · 24 hydrogen bonds · protein-protein
- L–H · 1558 Ų buried · 28 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 7 disulfide (disulfide).
Compared structures
- 1HRT · The structure of a complex of bovine alpha-thrombin and recombinant hirudin at 2.8… · the same entry in another collection · chain L against L, TM-score 1.00
- P00735 · AlphaFold monomer V2.0 prediction for prothrombin (P00735) · a predicted model of the same protein · chain H against A, TM-score 0.96
- P01050 · AlphaFold monomer V2.0 prediction for hirudin variant-1 (P01050) · a predicted model of the same protein · chain I against A, TM-score 0.82
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 P00735
- Every structure of UniProt P01050
- Elsewhere: RCSB PDB 1HRT · PDBe 1HRT · UniProt P00735 · UniProt P01050
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