Research workbench
Human factor viia-tissue factor complexed with ethylsulfonamide-D-5- (3-carboxybenzyloxy)-TRP-gln-P-aminobenzamidine
Analyse Human factor viia-tissue factor complexed with ethylsulfonamide-D-5… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2ZZU
- Type
- protein
- Length
- 587 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Factor VII light chain; Factor VII heavy chain; Tissue factor
- EC
- 3.4.21.21
- UniProt
- P08709, P13726
- Ligands
- 359, BGC, FUC, CA
- Pockets
- 9 · best druggability 0.54
Structure
x-ray diffraction · 3 distinct chains · 16% helix, 37% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| L | Factor VII light chain (EC 3.4.21.21) | protein | 142 | 27% helix, 18% strand | P08709 |
| H | Factor VII heavy chain (EC 3.4.21.21) | protein | 254 | 14% helix, 37% strand | P08709 |
| T | Tissue factor | protein | 191 | 8% helix, 51% strand | P13726 |
Ligands and binding sites
- 359 · 3-[[3-[(2R)-3-[[(2S)-5-amino-1-[(4-carbamimidoylphenyl)methylamino]-1,5-dioxo-pentan-2-yl]amino]-2-(ethylsulfonylamino)-3-oxo-propyl]-1H-indol-5-yl]oxymethyl]benzoic acid · ligand · chains H
- BGC · beta-D-glucopyranose · sugar · chains L
- FUC · alpha-L-fucopyranose · sugar · chains L, T
- 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
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 | 201 | 0.54 | 0.79 | 33 | empty |
| 2 | 90 | 0.54 | 0.84 | 17 | empty |
| 3 | 161 | 0.49 | 0.77 | 23 | empty |
| 4 | 114 | 0.48 | 0.80 | 25 | empty |
| 5 | 91 | 0.47 | 0.81 | 24 | 359 |
Interfaces
3 interfaces between chains.
- L–T · 1463 Ų buried · 17 hydrogen bonds · protein-protein
- L–H · 1024 Ų buried · 17 hydrogen bonds · protein-protein
- H–T · 580 Ų buried · 14 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 13 disulfide, 10 modified, 2 glycan (disulfide, carboxylation, O-glycosylation).
Compared structures
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 2ZZU · PDBe 2ZZU · UniProt P08709 · UniProt P13726
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