Research workbench
Contact pathway inhibitor from a sand fly
Analyse Contact pathway inhibitor from a sand fly in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4JD9
- Type
- protein
- Length
- 832 residues
- Chains
- 7
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 14.5 kda salivary protein
- UniProt
- Q06K46
- Ligands
- SO4
- Pockets
- 18 · best druggability 0.65
Structure
x-ray diffraction · 3 distinct chains · 67% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, E | 14.5 kda salivary protein | protein | 118 | 67% helix, 0% strand | Q06K46 |
| B, C, D, F | 14.5 kda salivary protein | protein | 119 | 68% helix, 0% strand | Q06K46 |
| G | 14.5 kda salivary protein | protein | 120 | 65% helix, 0% strand | Q06K46 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 43 copies · chains A, C, D, B, F, E, G
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
18 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 294 | 0.65 | 0.81 | 37 | empty |
| 2 | 245 | 0.64 | 0.82 | 30 | empty |
| 3 | 277 | 0.64 | 0.81 | 37 | empty |
| 4 | 261 | 0.64 | 0.81 | 31 | empty |
| 5 | 294 | 0.63 | 0.80 | 36 | empty |
Interfaces
6 interfaces between chains.
- B–C · 928 Ų buried · 14 hydrogen bonds · protein-protein
- B–F · 876 Ų buried · 13 hydrogen bonds · protein-protein
- A–C · 868 Ų buried · 15 hydrogen bonds · protein-protein
- A–D · 827 Ų buried · 18 hydrogen bonds · protein-protein
- E–G · 820 Ų buried · 14 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 21 disulfide (disulfide).
Compared structures
- 4JD9 · Contact pathway inhibitor from a sand fly · the same entry in another collection · chain A against A, TM-score 1.00
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 Q06K46
- Elsewhere: RCSB PDB 4JD9 · PDBe 4JD9 · UniProt Q06K46
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