MolNFT v1 · #19269 · protein
Structure of human factor viia and its implications for the triggering of blood coagulation
1QFK · Coagulation factor viia light chain: “Structure of human factor viia and its implications for the triggering of blood coagulation”. X-ray diffraction, 6 ligands (0Z6, NAG, FUL), 2 pockets (best druggability 0.44). MolNFT v1 #19269…
- PDB
- 1QFK
- Type
- protein
- Length
- 348 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Coagulation factor viia light chain; Coagulation factor viia heavy chain
- EC
- 3.4.21.21
- UniProt
- P08709
- Ligands
- 0Z6, NAG, FUL, GLC, FUC, CA
- Pockets
- 2 · best druggability 0.44
Structure
x-ray diffraction · 2 distinct chains · 12% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| L | Coagulation factor viia light chain (EC 3.4.21.21) | protein | 96 | 15% helix, 23% strand | P08709 |
| H | Coagulation factor viia heavy chain (EC 3.4.21.21) | protein | 252 | 11% helix, 37% strand | P08709 |
Ligands and binding sites
- 0Z6 · D-phenylalanyl-N-[(2S,3S)-6-{[amino(iminio)methyl]amino}-1-chloro-2-hydroxyhexan-3-yl]-L-phenylalaninamide · ligand · chains H
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains H
- FUL · beta-L-fucopyranose · sugar
- GLC · alpha-D-glucopyranose · sugar · chains L
- FUC · alpha-L-fucopyranose · sugar · chains L
- CA · Calcium ion · metal · chains H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 146 | 0.44 | 0.75 | 23 | empty |
| 2 | 117 | 0.43 | 0.77 | 27 | 0Z6 |
Interfaces
1 interface between chains.
- L–H · 1017 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 11 disulfide, 3 glycan, 2 covalent (disulfide, covalent ligand, O-glycosylation, N-glycosylation).
Compared structures
- 1QFK · Structure of human factor viia and its implications for the triggering of blood… · 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
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 1QFK · PDBe 1QFK · UniProt P08709
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