MolNFT v1 · #122324 · protein
Crystal structure of photoreceptor dehydrogenase from drosophila melanogaster
5ILO · Photoreceptor dehydrogenase, isoform C: “Crystal structure of photoreceptor dehydrogenase from drosophila melanogaster”. X-ray diffraction, 1 ligand (NAD), 6 pockets (best druggability 0.72). MolNFT v1 #122324 on GenesisL1: 3D…
- PDB
- 5ILO
- Type
- protein
- Length
- 520 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Photoreceptor dehydrogenase, isoform C
- EC
- 1.1.1.1, 1.1.1.105
- UniProt
- Q7KNR7
- Ligands
- NAD
- Pockets
- 6 · best druggability 0.72
Structure
x-ray diffraction · 2 distinct chains · 45% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Photoreceptor dehydrogenase, isoform C (EC 1.1.1.1, 1.1.1.105) | protein | 256 | 43% helix, 18% strand | Q7KNR7 |
| B | Photoreceptor dehydrogenase, isoform C (EC 1.1.1.1, 1.1.1.105) | protein | 264 | 47% helix, 17% strand | Q7KNR7 |
Ligands and binding sites
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 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, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 209 | 0.72 | 0.88 | 34 | empty |
| 2 | 439 | 0.69 | 0.80 | 55 | NAD |
| 3 | 367 | 0.65 | 0.79 | 45 | NAD |
| 4 | 145 | 0.49 | 0.78 | 23 | empty |
| 5 | 132 | 0.43 | 0.76 | 31 | empty |
Interfaces
1 interface between chains.
- A–B · 2440 Ų buried · 17 hydrogen bonds · protein-protein
Compared structures
- 5ILO · Crystal structure of photoreceptor dehydrogenase from Drosophila melanogaster · 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 Q7KNR7
- Elsewhere: RCSB PDB 5ILO · PDBe 5ILO · UniProt Q7KNR7
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