MolNFT v1 · #122317 · protein
Crystal structure of photoreceptor dehydrogenase from drosophila melanogaster
5ILG · Photoreceptor dehydrogenase, isoform C: “Crystal structure of photoreceptor dehydrogenase from drosophila melanogaster”. X-ray diffraction, 3 ligands (NAD, IPH, MG), 5 pockets (best druggability 0.74). MolNFT v1 #122317 on…
- PDB
- 5ILG
- Type
- protein
- Length
- 523 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, IPH, MG
- Pockets
- 5 · best druggability 0.74
Structure
x-ray diffraction · 2 distinct chains · 48% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Photoreceptor dehydrogenase, isoform C (EC 1.1.1.1, 1.1.1.105) | protein | 265 | 47% helix, 18% strand | Q7KNR7 |
| B | Photoreceptor dehydrogenase, isoform C (EC 1.1.1.1, 1.1.1.105) | protein | 258 | 48% helix, 19% strand | Q7KNR7 |
Ligands and binding sites
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 2 copies · chains A, B
- IPH · Phenol · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 2 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 3 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 224 | 0.74 | 0.89 | 27 | empty |
| 2 | 448 | 0.71 | 0.81 | 51 | NAD, IPH |
| 3 | 477 | 0.71 | 0.81 | 53 | MG, NAD, IPH, EDO |
| 4 | 206 | 0.53 | 0.77 | 28 | empty |
| 5 | 166 | 0.50 | 0.77 | 24 | empty |
Interfaces
1 interface between chains.
- A–B · 2457 Ų buried · 13 hydrogen bonds · protein-protein
Compared structures
- 5ILG · 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 5ILG · PDBe 5ILG · UniProt Q7KNR7
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