Research workbench
Human Factor Viia-Tissue Factor Complexed with propylsulfonamide-D-Thr-Met-p-aminobenzamidine
Analyse Human Factor Viia-Tissue Factor Complexed with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1WQV
- Type
- protein
- Length
- 587 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.5
- Source
- Homo sapiens
- Molecule
- Coagulation factor VII; Tissue factor
- EC
- 3.4.21.21
- UniProt
- P08709, P13726
- Ligands
- PSM, BGC, FUC, CA
- Pockets
- 8 · best druggability 0.58
Structure
x-ray diffraction · resolution 2.5 · 3 distinct chains · 16% helix, 37% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| L | Coagulation factor VII (EC 3.4.21.21) | protein | 142 | 30% helix, 18% strand | P08709 |
| H | Coagulation factor VII (EC 3.4.21.21) | protein | 254 | 15% helix, 37% strand | P08709 |
| T | Tissue factor | protein | 191 | 8% helix, 50% strand | P13726 |
Ligands and binding sites
- PSM · N-[dihydroxy(propyl)-lambda~4~-sulfanyl]threonyl-N~1~-{4-[amino(imino)methyl]benzyl}methioninamide · ligand · chains H
- BGC · beta-D-glucopyranose · sugar · chains L
- FUC · alpha-L-fucopyranose · sugar · chains L, T
- CA · Calcium ion · metal · 9 copies · chains L, 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, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 247 | 0.58 | 0.79 | 43 | PSM |
| 2 | 205 | 0.54 | 0.78 | 36 | empty |
| 3 | 164 | 0.49 | 0.78 | 23 | empty |
| 4 | 121 | 0.48 | 0.79 | 26 | empty |
| 5 | 110 | 0.46 | 0.79 | 22 | empty |
Interfaces
3 interfaces between chains.
- L–T · 1456 Ų buried · 16 hydrogen bonds · protein-protein
- L–H · 1029 Ų buried · 15 hydrogen bonds · protein-protein
- H–T · 584 Ų buried · 13 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 disulfide, 10 modified, 2 glycan (disulfide, carboxylation, O-glycosylation).
Compared structures
- 1WQV · Human factor viia-tissue factor complexed with propylsulfonamide-D… · the same entry in another collection · chain H against H, TM-score 1.00
- P13726 · AlphaFold monomer V2.0 prediction for tissue factor (P13726) · a predicted model of the same protein · chain T against A, TM-score 0.99
- 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
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 1WQV · PDBe 1WQV · UniProt P08709 · UniProt P13726
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.