Research workbench
Factor viia in complex with the inhibitor (11R)-11-[(1- aminoisoquinolin-6-YL)AMINO]-16-(cyclopropylsulfonyl)-13-methyl-2,13- DIAZATRICYCLO[13.3.1.1~6,10~]ICOSA-1(19),6(20),7,9,15,17-hexaene-3, 12-dione
Analyse Factor viia in complex with the inhibitor (11R)-11-[(1… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5TQF
- Type
- protein
- Length
- 305 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Factor viia (heavy chain); Factor viia (light chain)
- EC
- 3.4.21.21
- UniProt
- P08709
- Ligands
- 7KR, CA, SO4
- Pockets
- 3 · best druggability 0.44
Structure
x-ray diffraction · 2 distinct chains · 15% helix, 35% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| H | Factor viia (heavy chain) (EC 3.4.21.21) | protein | 250 | 15% helix, 37% strand | P08709 |
| L | Factor viia (light chain) (EC 3.4.21.21) | protein | 55 | 16% helix, 25% strand | P08709 |
Ligands and binding sites
- 7KR · (11R)-11-[(1-aminoisoquinolin-6-yl)amino]-16-(cyclopropylsulfonyl)-13-methyl-2,13-diazatricyclo[13.3.1.1~6,10~]icosa-1(19),6(20),7,9,15, 17-hexaene-3,12-dione · ligand · chains H
- CA · Calcium ion · metal · chains H
- SO4 · Sulfate ion · ion · 4 copies · chains H, L
- GOL · Glycerol · additive · 3 copies · chains H, L
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 116 | 0.44 | 0.78 | 30 | 7KR, GOL |
| 2 | 102 | 0.38 | 0.75 | 15 | SO4 |
| 3 | 68 | 0.37 | 0.78 | 14 | SO4 |
Interfaces
1 interface between chains.
- H–L · 1055 Ų buried · 15 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
- 5TQF · Factor VIIa in complex with the inhibitor (11R)-11-[(1-aminoisoquinolin-6-yl)amino]-16-(cy… · the same entry in another collection · chain H against H, 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
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
- Elsewhere: RCSB PDB 5TQF · PDBe 5TQF · UniProt P08709
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