MolNFT v1 · #16656 · protein
Dissecting and designing inhibitor selectivity determinants at the S1 site using an artificial ALA190 protease (ALA190 upa)
1O5G · Prothrombin: “Dissecting and designing inhibitor selectivity determinants at the S1 site using an artificial ALA190…”. X-ray diffraction, 3 ligands (CR9, NA, CA), 1 pocket (best druggability 0.56). MolNFT v1 #16656 on GenesisL1: 3D…
- PDB
- 1O5G
- Type
- protein
- Length
- 294 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Prothrombin; Hirudin iiib'
- EC
- 3.4.21.5
- UniProt
- P00734, P28511
- Ligands
- CR9, NA, CA
- Pockets
- 1 · best druggability 0.56
Structure
x-ray diffraction · 3 distinct chains · 17% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| L | Prothrombin (EC 3.4.21.5) | protein | 33 | 30% helix, 0% strand | P00734 |
| H | Prothrombin (EC 3.4.21.5) | protein | 250 | 14% helix, 34% strand | P00734 |
| I | Hirudin iiib' | protein | 11 | 27% helix, 0% strand | P28511 |
Ligands and binding sites
- CR9 · 2-{5-[amino(iminio)methyl]-6-fluoro-1H-benzimidazol-2-yl}-6-[(2-methylcyclohexyl)oxy]benzenolate · ligand · chains H
- NA · Sodium ion · metal · chains H
- CA · Calcium ion · metal · 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 | 317 | 0.56 | 0.76 | 42 | CR9 |
Interfaces
2 interfaces between chains.
- L–H · 1400 Ų buried · 34 hydrogen bonds · protein-protein
- H–I · 685 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide, 1 modified (disulfide, sulfation).
Compared structures
- 1O5G · Dissecting and Designing Inhibitor Selectivity Determinants at the S1 site Using an… · the same entry in another collection · chain L against L, TM-score 1.00
- P28511 · AlphaFold monomer V2.0 prediction for hirudin-3B' (P28511) · a predicted model of the same protein · chain I against A, TM-score 0.44
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 P28511
- Elsewhere: RCSB PDB 1O5G · PDBe 1O5G · UniProt P00734 · UniProt P28511
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