Research workbench
Crystal structure analysis of human factor viia , souluble tissue factor complexed with bcx-3607
Analyse Crystal structure analysis of human factor viia , souluble tissue factor… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2EC9
- Type
- protein
- Length
- 587 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Coagulation factor VII; Tissue factor
- EC
- 3.4.21.21
- UniProt
- P08709, P13726
- Ligands
- ASO, 24X, FUC, CA
- Pockets
- 8 · best druggability 0.51
Structure
x-ray diffraction · 4 distinct chains · 14% helix, 36% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| L | Coagulation factor VII (EC 3.4.21.21) | protein | 142 | 23% helix, 18% strand | P08709 |
| H | Coagulation factor VII (EC 3.4.21.21) | protein | 254 | 13% helix, 36% strand | P08709 |
| T | Tissue factor | protein | 75 | 5% helix, 57% strand | P13726 |
| U | Tissue factor | protein | 116 | 10% helix, 46% strand | P13726 |
Ligands and binding sites
- ASO · 1,5-anhydro-D-glucitol · ligand · chains L
- 24X · 2'-((5-carbamimidoylpyridin-2-ylamino)methyl)-4-(isobutylcarbamoyl)-4'-vinylbiphenyl-2-carboxylic acid · ligand · chains H
- FUC · alpha-L-fucopyranose · sugar · chains L, U
- CA · Calcium ion · metal · 9 copies · chains L, 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, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 81 | 0.51 | 0.83 | 17 | empty |
| 2 | 154 | 0.49 | 0.78 | 22 | empty |
| 3 | 151 | 0.48 | 0.78 | 22 | empty |
| 4 | 101 | 0.46 | 0.79 | 19 | empty |
| 5 | 98 | 0.45 | 0.80 | 21 | empty |
Interfaces
6 interfaces between chains.
- T–U · 1246 Ų buried · 23 hydrogen bonds · protein-protein
- L–H · 1049 Ų buried · 18 hydrogen bonds · protein-protein
- L–U · 899 Ų buried · 7 hydrogen bonds · protein-protein
- L–T · 657 Ų buried · 8 hydrogen bonds · protein-protein
- H–T · 352 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 14 disulfide, 10 modified (disulfide, carboxylation).
Compared structures
- 2EC9 · Crystal structure analysis of human Factor VIIa , Souluble tissue factor complexed with… · the same entry in another collection · chain U against U, 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 0.98
- 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 2EC9 · PDBe 2EC9 · UniProt P08709 · UniProt P13726
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