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Crystal structure of juvenile hormone binding protein from silkworm
Analyse Crystal structure of juvenile hormone binding protein from silkworm in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3A1Z
- Type
- protein
- Length
- 841 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hemolymph juvenile hormone binding protein
- UniProt
- Q9U556
- Ligands
- ZN
- Pockets
- 14 · best druggability 0.81
Structure
x-ray diffraction · 4 distinct chains · 32% helix, 43% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Hemolymph juvenile hormone binding protein | protein | 208 | 33% helix, 43% strand | Q9U556 |
| B | Hemolymph juvenile hormone binding protein | protein | 212 | 31% helix, 43% strand | Q9U556 |
| C | Hemolymph juvenile hormone binding protein | protein | 212 | 32% helix, 43% strand | Q9U556 |
| D | Hemolymph juvenile hormone binding protein | protein | 209 | 33% helix, 44% strand | Q9U556 |
Ligands and binding sites
- ZN · Zinc ion · metal · 20 copies · chains A, C, B, D
- MPD · (4S)-2-methyl-2,4-pentanediol · additive · 8 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 630 | 0.81 | 0.86 | 69 | empty |
| 2 | 131 | 0.80 | 0.97 | 21 | MPD |
| 3 | 605 | 0.78 | 0.84 | 62 | empty |
| 4 | 256 | 0.75 | 0.88 | 29 | MPD |
| 5 | 205 | 0.73 | 0.88 | 26 | MPD |
Interfaces
6 interfaces between chains.
- B–D · 569 Ų buried · 11 hydrogen bonds · protein-protein
- A–C · 557 Ų buried · 11 hydrogen bonds · protein-protein
- C–D · 426 Ų buried · 7 hydrogen bonds · protein-protein
- A–B · 411 Ų buried · 5 hydrogen bonds · protein-protein
- A–D · 97 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
- 3A1Z · Crystal structure of juvenile hormone binding protein from silkworm · 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 Q9U556
- Elsewhere: RCSB PDB 3A1Z · PDBe 3A1Z · UniProt Q9U556
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