MolNFT v1 · #28810 · protein
X-ray crystal structure of thrombin inhibited by synthetic cyanopeptide analogue ra-1008
1YPL · Thrombin light chain: “X-ray crystal structure of thrombin inhibited by synthetic cyanopeptide analogue ra-1008”. X-ray diffraction, 2 ligands (RA8, NA), 1 pocket (best druggability 0.54). MolNFT v1 #28810 on GenesisL1: 3D…
- PDB
- 1YPL
- Type
- protein
- Length
- 287 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Thrombin light chain; Thrombin heavy chain; Hirudin
- EC
- 3.4.21.5
- UniProt
- P00734, P28504
- Ligands
- RA8, NA
- Pockets
- 1 · best druggability 0.54
Structure
x-ray diffraction · 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 | 27 | 37% helix, 0% strand | P00734 |
| H | Thrombin heavy chain (EC 3.4.21.5) | protein | 250 | 16% helix, 35% strand | P00734 |
| I | Hirudin | protein | 10 | 30% helix, 0% strand | P28504 |
Ligands and binding sites
- RA8 · N-(benzylsulfonyl)-L-leucyl-N-(4-{[amino(imino)methyl]amino}butyl)-L-prolinamide · ligand · chains H
- NA · Sodium ion · metal · 2 copies · chains H
- GOL · Glycerol · additive · 2 copies · chains H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 248 | 0.54 | 0.76 | 37 | RA8 |
Interfaces
2 interfaces between chains.
- L–H · 1068 Ų buried · 27 hydrogen bonds · protein-protein
- H–I · 593 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide, 1 modified (disulfide, sulfation).
Compared structures
- 1YPL · X-ray crystal structure of thrombin inhibited by synthetic cyanopeptide analogue RA-1008 · the same entry in another collection · chain I against I, TM-score 1.00
- P28504 · AlphaFold monomer V2.0 prediction for hirudin-2 (P28504) · a predicted model of the same protein · chain I against A, TM-score 0.52
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 P28504
- Elsewhere: RCSB PDB 1YPL · PDBe 1YPL · UniProt P00734 · UniProt P28504
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