MolNFT v1 · #11951 · protein
Human thrombin-inhibitor complex
1K22 · Prothrombin: “Human thrombin-inhibitor complex”. X-ray diffraction, 3 ligands (MEL, NAG, NA), 4 pockets (best druggability 0.50). MolNFT v1 #11951 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 1K22
- Type
- protein
- Length
- 290 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Prothrombin; Hirudin variant-2
- EC
- 3.4.21.5
- UniProt
- P00734, P09945
- Ligands
- MEL, NAG, NA
- Pockets
- 4 · best druggability 0.50
Structure
x-ray diffraction · 3 distinct chains · 18% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| L | Prothrombin (EC 3.4.21.5) | protein | 29 | 34% helix, 0% strand | P00734 |
| H | Prothrombin (EC 3.4.21.5) | protein | 251 | 16% helix, 35% strand | P00734 |
| I | Hirudin variant-2 | protein | 10 | 30% helix, 0% strand | P09945 |
Ligands and binding sites
- MEL · [((1R)-2-{(2S)-2-[({4-[amino(imino)methyl]benzyl}amino)carbonyl]azetidinyl}-1-cyclohexyl-2-oxoethyl)amino]acetic acid · ligand · chains H
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · 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
4 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 148 | 0.50 | 0.78 | 24 | MEL |
| 2 | 52 | 0.33 | 0.78 | 16 | empty |
| 3 | 55 | 0.30 | 0.76 | 19 | empty |
| 4 | 59 | 0.29 | 0.74 | 12 | empty |
Interfaces
2 interfaces between chains.
- L–H · 1195 Ų buried · 27 hydrogen bonds · protein-protein
- H–I · 692 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 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 1K22 · PDBe 1K22 · UniProt P00734 · UniProt P09945
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.