Research workbench
TF7A_3771 complex
Analyse TF7A_3771 complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1W0Y
- 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
- 771, FUC, BGC, CA
- Pockets
- 9 · best druggability 0.59
Structure
x-ray diffraction · 3 distinct chains · 16% helix, 37% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| H | Blood coagulation factor viia (EC 3.4.21.21) | protein | 251 | 15% helix, 37% strand | P08709 |
| L | Blood coagulation factor viia (EC 3.4.21.21) | protein | 142 | 27% helix, 18% strand | P08709 |
| T | Tissue factor | protein | 188 | 9% helix, 51% strand | P13726 |
Ligands and binding sites
- 771 · 4-(4-benzyloxy-2-methanesulfonylamino-5-methoxy-benzylamino)-benzamidine · 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
9 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 315 | 0.59 | 0.77 | 48 | empty |
| 2 | 175 | 0.53 | 0.79 | 27 | empty |
| 3 | 69 | 0.47 | 0.83 | 15 | CAC |
| 4 | 107 | 0.45 | 0.79 | 22 | empty |
| 5 | 120 | 0.44 | 0.77 | 19 | empty |
Interfaces
3 interfaces between chains.
- L–T · 1347 Ų buried · 15 hydrogen bonds · protein-protein
- H–L · 1014 Ų buried · 14 hydrogen bonds · protein-protein
- H–T · 580 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 14 disulfide, 9 modified, 2 glycan (disulfide, carboxylation, O-glycosylation).
Compared structures
- 1W0Y · tf7a_3771 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 1W0Y · PDBe 1W0Y · UniProt P08709 · UniProt P13726
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