Research workbench
Mosquito juvenile hormone-binding protein
Analyse Mosquito juvenile hormone-binding protein in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5V13
- Type
- protein
- Length
- 803 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- AAEL008620-pa odorant-binding protein
- UniProt
- Q16Y94
- Ligands
- JH3
- Pockets
- 9 · best druggability 0.88
Structure
x-ray diffraction · 2 distinct chains · 60% helix, 2% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | AAEL008620-pa odorant-binding protein | protein | 267 | 60% helix, 2% strand | Q16Y94 |
| A, C | AAEL008620-pa odorant-binding protein | protein | 268 | 60% helix, 2% strand | Q16Y94 |
Ligands and binding sites
- JH3 · methyl (2E,6E)-9-[(2R)-3,3-dimethyloxiran-2-yl]-3,7-dimethylnona-2,6-dienoate · ligand · 3 copies · chains B, A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 940 | 0.88 | 0.89 | 123 | JH3 |
| 2 | 420 | 0.85 | 0.93 | 62 | empty |
| 3 | 257 | 0.84 | 0.95 | 41 | JH3 |
| 4 | 691 | 0.73 | 0.79 | 60 | empty |
| 5 | 698 | 0.72 | 0.79 | 71 | empty |
Interfaces
3 interfaces between chains.
- B–C · 850 Ų buried · 14 hydrogen bonds · protein-protein
- A–C · 836 Ų buried · 12 hydrogen bonds · protein-protein
- B–A · 826 Ų buried · 13 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 disulfide (disulfide).
Compared structures
- 5V13 · Mosquito juvenile hormone-binding protein · the same entry in another collection · chain B against B, 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 Q16Y94
- Elsewhere: RCSB PDB 5V13 · PDBe 5V13 · UniProt Q16Y94
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