MolNFT v1 · #4023 · protein
Complex of active site inhibited human blood coagulation factor viia with human recombinant soluble tissue factor
1DAN · Blood coagulation factor viia light chain: “Complex of active site inhibited human blood coagulation factor viia with human recombinant soluble tissue…”. X-ray diffraction, 5 ligands (0Z6, BGC, FUC), 8 pockets (best druggability…
- 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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