MolNFT v1 · #61692 · protein
Understanding thrombin inhibition
3DT0 · Thrombin light chain: “Understanding thrombin inhibition”. X-ray diffraction, 2 ligands (16U, NA), 2 pockets (best druggability 0.56). MolNFT v1 #61692 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 3DT0
- Type
- protein
- Length
- 285 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Thrombin light chain; Thrombin heavy chain; Hirudin variant-1
- EC
- 3.4.21.5
- UniProt
- P00734, P01050
- Ligands
- 16U, NA
- Pockets
- 2 · best druggability 0.56
Structure
x-ray diffraction · 3 distinct chains · 16% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| L | Thrombin light chain (EC 3.4.21.5) | protein | 26 | 38% helix, 0% strand | P00734 |
| H | Thrombin heavy chain (EC 3.4.21.5) | protein | 250 | 14% helix, 34% strand | P00734 |
| I | Hirudin variant-1 | protein | 9 | 0% helix, 0% strand | P01050 |
Ligands and binding sites
- 16U · N-(3-chlorobenzyl)-1-(4-methylpentanoyl)-L-prolinamide · ligand · chains H
- NA · Sodium ion · metal · 2 copies · 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 | 282 | 0.56 | 0.77 | 39 | 16U |
| 2 | 63 | 0.29 | 0.74 | 15 | empty |
Interfaces
2 interfaces between chains.
- L–H · 1057 Ų buried · 29 hydrogen bonds · protein-protein
- H–I · 548 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide, 1 modified (disulfide, 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 P01050
- Elsewhere: RCSB PDB 3DT0 · PDBe 3DT0 · UniProt P00734 · UniProt P01050
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.