Research workbench
Crystal structure of a ternary complex of factor VIIA/TISSUE factor and 2-[[6-[3-(AMINOIMINOMETHYL)PHENOXY]-3,5-difluro-4-[(1-methyl-3- PHENYLPROPYL)AMINO]-2-PYRIDINYL]OXY]-benzoic acid
Analyse Crystal structure of a ternary complex of factor VIIA/TISSUE factor and… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2AEI
- Type
- protein
- Length
- 591 residues
- Chains
- 3
- 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
- 03R, CA
- Pockets
- 11 · best druggability 0.60
Structure
x-ray diffraction · 3 distinct chains · 15% helix, 37% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| L | Coagulation factor VII (EC 3.4.21.21) | protein | 142 | 29% helix, 17% strand | P08709 |
| H | Coagulation factor VII (EC 3.4.21.21) | protein | 254 | 13% helix, 37% strand | P08709 |
| T | Tissue factor | protein | 195 | 8% helix, 51% strand | P13726 |
Ligands and binding sites
- 03R · 2-({6-{3-[amino(imino)methyl]phenoxy}-3,5-difluoro-4-[(1-methyl-3-phenylpropyl)amino]-2-pyridinyl}oxy)benzoic acid · ligand · chains H
- CA · Calcium ion · metal · 8 copies · chains L, H
- CAC · Cacodylate ion · additive · chains H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 218 | 0.60 | 0.81 | 31 | empty |
| 2 | 153 | 0.51 | 0.79 | 27 | empty |
| 3 | 64 | 0.49 | 0.85 | 17 | CAC |
| 4 | 165 | 0.49 | 0.77 | 21 | empty |
| 5 | 110 | 0.44 | 0.78 | 23 | empty |
Interfaces
3 interfaces between chains.
- L–T · 1352 Ų buried · 18 hydrogen bonds · protein-protein
- L–H · 1002 Ų buried · 12 hydrogen bonds · protein-protein
- H–T · 543 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 14 disulfide, 10 modified (disulfide, carboxylation).
Compared structures
- 2AEI · Crystal structure of a ternary complex of factor VIIa/tissue factor and… · the same entry in another collection · chain L against L, 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 2AEI · PDBe 2AEI · UniProt P08709 · UniProt P13726
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