Research workbench
TF7A_4380 complex
Analyse TF7A_4380 complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1W2K
- Type
- protein
- Length
- 581 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Blood coagulation factor viia; Tissue factor
- EC
- 3.4.21.21
- UniProt
- P08709, P13726
- Ligands
- 380, FUC, BGC, CA
- Pockets
- 8 · best druggability 0.62
Structure
x-ray diffraction · 3 distinct chains · 16% helix, 36% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| H | Blood coagulation factor viia (EC 3.4.21.21) | protein | 251 | 13% helix, 37% strand | P08709 |
| L | Blood coagulation factor viia (EC 3.4.21.21) | protein | 142 | 30% helix, 18% strand | P08709 |
| T | Tissue factor | protein | 188 | 9% helix, 49% strand | P13726 |
Ligands and binding sites
- 380 · (2R)-2-({4-[amino(imino)methyl]phenyl}amino)-N-benzyl-2-(3,4-dimethoxyphenyl)acetamide · ligand · chains H
- FUC · alpha-L-fucopyranose · sugar · chains L, T
- BGC · beta-D-glucopyranose · sugar · chains L
- CA · Calcium ion · metal · 9 copies · chains H, L
- 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, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 382 | 0.62 | 0.78 | 45 | empty |
| 2 | 128 | 0.50 | 0.80 | 24 | empty |
| 3 | 116 | 0.46 | 0.79 | 20 | empty |
| 4 | 146 | 0.45 | 0.76 | 23 | empty |
| 5 | 77 | 0.44 | 0.81 | 16 | CAC |
Interfaces
3 interfaces between chains.
- L–T · 1325 Ų buried · 15 hydrogen bonds · protein-protein
- H–L · 1017 Ų buried · 14 hydrogen bonds · protein-protein
- H–T · 568 Ų buried · 14 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 14 disulfide, 9 modified, 2 glycan (disulfide, carboxylation, O-glycosylation).
Compared structures
- 1W2K · tf7a_4380 complex · the same entry in another collection · chain H against H, 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 1W2K · PDBe 1W2K · UniProt P08709 · UniProt P13726
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