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Structure of human factor viia and its implications for the triggering of blood coagulation
Analyse Structure of human factor viia and its implications for the triggering of blood… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- 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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