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
- 1O5D
- Type
- protein
- Length
- 501 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Coagulation factor VII; Tissue factor
- EC
- 3.4.21.21
- UniProt
- P08709, P13726
- Ligands
- CR9
- Pockets
- 8 · best druggability 0.69
Structure
x-ray diffraction · 3 distinct chains · 12% helix, 38% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| L | Coagulation factor VII (EC 3.4.21.21) | protein | 96 | 14% helix, 30% strand | P08709 |
| H | Coagulation factor VII (EC 3.4.21.21) | protein | 254 | 13% helix, 37% strand | P08709 |
| T | Tissue factor | protein | 151 | 9% helix, 45% strand | P13726 |
Ligands and binding sites
- CR9 · 2-{5-[amino(iminio)methyl]-6-fluoro-1H-benzimidazol-2-yl}-6-[(2-methylcyclohexyl)oxy]benzenolate · ligand · chains H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 323 | 0.69 | 0.83 | 48 | empty |
| 2 | 149 | 0.45 | 0.76 | 22 | empty |
| 3 | 64 | 0.45 | 0.82 | 17 | empty |
| 4 | 139 | 0.44 | 0.76 | 20 | empty |
| 5 | 95 | 0.44 | 0.79 | 25 | empty |
Interfaces
3 interfaces between chains.
- L–H · 1006 Ų buried · 13 hydrogen bonds · protein-protein
- L–T · 893 Ų buried · 12 hydrogen bonds · protein-protein
- H–T · 689 Ų buried · 14 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 disulfide (disulfide).
Compared structures
- 1O5D · 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
- P08709 · AlphaFold monomer V2.0 prediction for coagulation factor VII (P08709) · a predicted model of the same protein · chain H against A, TM-score 0.97
- P13726 · AlphaFold monomer V2.0 prediction for tissue factor (P13726) · a predicted model of the same protein · chain T against A, TM-score 0.97
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 P08709
- Every structure of UniProt P13726
- Elsewhere: RCSB PDB 1O5D · PDBe 1O5D · UniProt P08709 · UniProt P13726
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