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Refined 2.3 ångströms X-ray crystal structure of bovine thrombin complexes formed with the benzamidine and arginine-based thrombin inhibitors napap, 4-tapap and mqpa: a starting point for improving antithrombotics
Analyse Refined 2.3 ångströms X-ray crystal structure of bovine thrombin complexes… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1ETT
- Type
- protein
- Length
- 295 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Epsilon-thrombin
- EC
- 3.4.21.5
- UniProt
- P00735
- Ligands
- 4QQ
- Pockets
- 3 · best druggability 0.58
Structure
x-ray diffraction · 2 distinct chains · 15% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| L | Epsilon-thrombin (EC 3.4.21.5) | protein | 36 | 39% helix, 3% strand | P00735 |
| H | Epsilon-thrombin (EC 3.4.21.5) | protein | 259 | 12% helix, 34% strand | P00735 |
Ligands and binding sites
- 4QQ · 4-[(2S)-2-{[(4-methylphenyl)sulfonyl]amino}-3-oxo-3-(piperidin-1-yl)propyl]benzene-1-carboximidamide · ligand · chains H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 394 | 0.58 | 0.75 | 42 | 4QQ |
| 2 | 51 | 0.55 | 0.90 | 24 | empty |
| 3 | 91 | 0.40 | 0.77 | 19 | empty |
Interfaces
1 interface between chains.
- L–H · 1390 Ų buried · 21 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 1ETT · Refined 2.3 ångströms X-ray crystal structure of bovine thrombin complexes formed with… · 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
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
- Elsewhere: RCSB PDB 1ETT · PDBe 1ETT · UniProt P00735
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