Research workbench
Dissecting and designing inhibitor selectivity determinants at the S1 site using an artificial ALA190 protease (ALA190 upa)
Analyse Dissecting and designing inhibitor selectivity determinants at the S1 site… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- 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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