MolNFT v1 · #50244 · protein
Crystal structure of juvenile hormone binding protein from galleria mellonella hemolymph
2RCK: “Crystal structure of juvenile hormone binding protein from galleria mellonella hemolymph”. X-ray diffraction, 2 ligands (NAG, SO4), 6 pockets (best druggability 0.70). MolNFT v1 #50244 on GenesisL1: 3D structure, binding sites and…
- PDB
- 2RCK
- Type
- protein
- Length
- 429 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Juvenile hormone binding protein
- UniProt
- Q8ITP4
- Ligands
- NAG, SO4
- Pockets
- 6 · best druggability 0.70
Structure
x-ray diffraction · 2 distinct chains · 33% helix, 43% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Juvenile hormone binding protein | protein | 221 | 33% helix, 40% strand | Q8ITP4 |
| B | Juvenile hormone binding protein | protein | 208 | 33% helix, 46% strand | Q8ITP4 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 2 copies · chains A, B
- GOL · Glycerol · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 549 | 0.70 | 0.79 | 52 | empty |
| 2 | 222 | 0.68 | 0.85 | 27 | empty |
| 3 | 262 | 0.67 | 0.83 | 28 | empty |
| 4 | 208 | 0.64 | 0.83 | 26 | empty |
| 5 | 234 | 0.62 | 0.80 | 27 | empty |
Interfaces
1 interface between chains.
- A–B · 645 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide, 2 glycan (disulfide, N-glycosylation).
Compared structures
- 2RCK · Crystal structure of juvenile hormone binding protein from Galleria mellonella hemolymph · 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 Q8ITP4
- Elsewhere: RCSB PDB 2RCK · PDBe 2RCK · UniProt Q8ITP4
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