MolNFT v1 · #185196 · protein
The X-ray structure of juvenile hormone diol kinase from the silk worm bombyx mori.
7PJD: “The X-ray structure of juvenile hormone diol kinase from the silk worm bombyx mori.”. X-ray diffraction, 1 ligand (CA), 16 pockets (best druggability 0.74). MolNFT v1 #185196 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 7PJD
- Type
- protein
- Length
- 1,092 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Juvenile hormone diol kinase
- UniProt
- Q6URH4
- Ligands
- CA
- Pockets
- 16 · best druggability 0.74
Structure
x-ray diffraction · 4 distinct chains · 66% helix, 5% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | Juvenile hormone diol kinase | protein | 183 | 67% helix, 5% strand | Q6URH4 |
| B | Juvenile hormone diol kinase | protein | 184 | 65% helix, 4% strand | Q6URH4 |
| C | Juvenile hormone diol kinase | protein | 178 | 65% helix, 6% strand | Q6URH4 |
| E, F | Juvenile hormone diol kinase | protein | 182 | 66% helix, 4% strand | Q6URH4 |
Ligands and binding sites
- CA · Calcium ion · metal · 18 copies · chains A, B, C, D, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 57 | 0.74 | 0.98 | 21 | empty |
| 2 | 763 | 0.74 | 0.79 | 74 | empty |
| 3 | 230 | 0.71 | 0.87 | 41 | empty |
| 4 | 293 | 0.70 | 0.84 | 49 | empty |
| 5 | 200 | 0.64 | 0.84 | 31 | empty |
Interfaces
10 interfaces between chains.
- C–D · 582 Ų buried · 9 hydrogen bonds · protein-protein
- D–F · 468 Ų buried · 4 hydrogen bonds · protein-protein
- A–D · 445 Ų buried · 5 hydrogen bonds · protein-protein
- A–B · 351 Ų buried · 6 hydrogen bonds · protein-protein
- B–C · 301 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 7PJD · The X-ray structure of juvenile hormone diol kinase from the silk worm Bombyx mori. · 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 Q6URH4
- Elsewhere: RCSB PDB 7PJD · PDBe 7PJD · UniProt Q6URH4
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.