Research workbench
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
- 1ETS
- 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
- MID
- Pockets
- 3 · best druggability 0.61
Structure
x-ray diffraction · 2 distinct chains · 16% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| L | Epsilon-thrombin (EC 3.4.21.5) | protein | 36 | 33% helix, 0% strand | P00735 |
| H | Epsilon-thrombin (EC 3.4.21.5) | protein | 259 | 14% helix, 36% strand | P00735 |
Ligands and binding sites
- MID · 1-[N-(naphthalen-2-ylsulfonyl)glycyl-4-carbamimidoyl-D-phenylalanyl]piperidine · 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, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 402 | 0.61 | 0.77 | 48 | MID |
| 2 | 85 | 0.40 | 0.78 | 17 | empty |
| 3 | 73 | 0.34 | 0.75 | 16 | empty |
Interfaces
1 interface between chains.
- L–H · 1353 Ų buried · 24 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 1ETS · 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 0.97
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 1ETS · PDBe 1ETS · UniProt P00735
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