Research workbench
Complex of active site inhibited human blood coagulation factor viia with human recombinant soluble tissue factor
Analyse Complex of active site inhibited human blood coagulation factor viia with human… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1DAN
- Type
- protein
- Length
- 587 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Blood coagulation factor viia light chain; Blood coagulation factor viia heavy chain…
- EC
- 3.4.21.21
- UniProt
- P08709, P13726
- Ligands
- 0Z6, BGC, FUC, CA, CL
- Pockets
- 8 · best druggability 0.61
Structure
x-ray diffraction · 4 distinct chains · 16% helix, 37% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| L | Blood coagulation factor viia light chain (EC 3.4.21.21) | protein | 142 | 32% helix, 18% strand | P08709 |
| H | Blood coagulation factor viia heavy chain (EC 3.4.21.21) | protein | 254 | 12% helix, 37% strand | P08709 |
| T | Soluble tissue factor | protein | 75 | 5% helix, 57% strand | P13726 |
| U | Soluble tissue factor | protein | 116 | 10% helix, 47% strand | P13726 |
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
- BGC · beta-D-glucopyranose · sugar · chains L
- FUC · alpha-L-fucopyranose · sugar · chains L, U
- CA · Calcium ion · metal · 9 copies · chains L, H
- CL · Chloride ion · ion · chains H
- CAC · Cacodylate ion · additive · chains 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, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 332 | 0.61 | 0.78 | 46 | empty |
| 2 | 90 | 0.51 | 0.83 | 17 | CAC |
| 3 | 125 | 0.50 | 0.80 | 23 | empty |
| 4 | 124 | 0.47 | 0.79 | 26 | empty |
| 5 | 117 | 0.43 | 0.77 | 26 | empty |
Interfaces
6 interfaces between chains.
- T–U · 1260 Ų buried · 22 hydrogen bonds · protein-protein
- L–H · 1040 Ų buried · 16 hydrogen bonds · protein-protein
- L–U · 884 Ų buried · 8 hydrogen bonds · protein-protein
- L–T · 645 Ų buried · 9 hydrogen bonds · protein-protein
- H–T · 344 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 14 disulfide, 10 modified, 2 covalent, 2 glycan (disulfide, carboxylation, covalent ligand, O-glycosylation).
Compared structures
- 1DAN · Complex of active site inhibited human blood coagulation factor VIIA with human… · the same entry in another collection · chain T against T, 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 1DAN · PDBe 1DAN · UniProt P08709 · UniProt P13726
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