Research workbench
Human tissue factor complexed with coagulation factor viia inhibited with a bpti-mutant
Analyse Human tissue factor complexed with coagulation factor viia inhibited with a… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1FAK
- Type
- protein
- Length
- 597 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein (blood coagulation factor viia); Protein (soluble tissue factor); Protein (5L15)
- EC
- 3.4.21.21
- UniProt
- P08709, P13726, P00974
- Ligands
- GLC, FUC, CA
- Pockets
- 9 · best druggability 0.64
Structure
x-ray diffraction · 4 distinct chains · 13% helix, 39% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| L | Protein (blood coagulation factor viia) (EC 3.4.21.21) | protein | 108 | 19% helix, 29% strand | P08709 |
| H | Protein (blood coagulation factor viia) (EC 3.4.21.21) | protein | 251 | 13% helix, 37% strand | P08709 |
| T | Protein (soluble tissue factor) | protein | 183 | 9% helix, 50% strand | P13726 |
| I | Protein (5L15) | protein | 55 | 20% helix, 29% strand | P00974 |
Ligands and binding sites
- GLC · alpha-D-glucopyranose · sugar · chains L
- FUC · alpha-L-fucopyranose · sugar · chains L, T
- CA · Calcium ion · metal · 2 copies · chains L, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 327 | 0.64 | 0.80 | 45 | empty |
| 2 | 181 | 0.49 | 0.77 | 36 | empty |
| 3 | 109 | 0.47 | 0.80 | 24 | empty |
| 4 | 144 | 0.45 | 0.76 | 17 | empty |
| 5 | 118 | 0.44 | 0.77 | 21 | empty |
Interfaces
4 interfaces between chains.
- L–T · 1215 Ų buried · 20 hydrogen bonds · protein-protein
- L–H · 1029 Ų buried · 15 hydrogen bonds · protein-protein
- H–I · 815 Ų buried · 25 hydrogen bonds · protein-protein
- H–T · 622 Ų buried · 13 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 16 disulfide, 2 glycan (disulfide, O-glycosylation).
Compared structures
- 1FAK · Human tissue factor complexed with coagulation factor viia inhibited with a bpti-mutant · the same entry in another collection · chain I against I, 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
- P00974 · AlphaFold monomer V2.0 prediction for pancreatic trypsin inhibitor (P00974) · a predicted model of the same protein · chain I 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
- Every structure of UniProt P00974
- Elsewhere: RCSB PDB 1FAK · PDBe 1FAK · UniProt P08709 · UniProt P13726 · UniProt P00974
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