Research workbench
Thrombin Inhibition by Pyridin Derivatives
Analyse Thrombin Inhibition by Pyridin Derivatives in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3QTO
- Type
- protein
- Length
- 290 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.52
- Source
- Homo sapiens; SYNTHETIC CONSTRUCT
- Molecule
- Thrombin light chain; Thrombin heavy chain; Hirudin variant-2
- EC
- 3.4.21.5
- UniProt
- P00734, P09945
- Ligands
- 10P, NAG, NA, PO4
- Pockets
- 2 · best druggability 0.54
Structure
x-ray diffraction · resolution 1.52 · 3 distinct chains · 18% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| L | Thrombin light chain (EC 3.4.21.5) | protein | 28 | 36% helix, 0% strand | P00734 |
| H | Thrombin heavy chain (EC 3.4.21.5) | protein | 251 | 16% helix, 35% strand | P00734 |
| I | Hirudin variant-2 | protein | 11 | 27% helix, 0% strand | P09945 |
Ligands and binding sites
- 10P · D-phenylalanyl-N-[(1-methylpyridinium-3-yl)methyl]-L-prolinamide · ligand · chains H
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · chains H
- NA · Sodium ion · metal · 2 copies · chains H
- PO4 · Phosphate ion · ion · chains H
- GOL · Glycerol · additive · 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 | 177 | 0.54 | 0.79 | 32 | 10P, GOL |
| 2 | 57 | 0.28 | 0.74 | 12 | empty |
Interfaces
2 interfaces between chains.
- L–H · 1111 Ų buried · 25 hydrogen bonds · protein-protein
- H–I · 651 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide, 1 glycan, 1 modified (disulfide, N-glycosylation, sulfation).
Compared structures
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 P09945
- Elsewhere: RCSB PDB 3QTO · PDBe 3QTO · UniProt P00734 · UniProt P09945
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