MolNFT v1 · #176388 · protein
The mutant E310G/A314Y of 3,5-dahdhcca complex with NADPH
7DL0 · 3,5-diaminohexanoate dehydrogenase: “The mutant E310G/A314Y of 3,5-dahdhcca complex with NADPH”. X-ray diffraction, 3 ligands (NAP, CL, SO4), 6 pockets (best druggability 0.78). MolNFT v1 #176388 on GenesisL1: 3D structure, binding…
- PDB
- 7DL0
- Type
- protein
- Length
- 706 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 3,5-diaminohexanoate dehydrogenase
- EC
- 1.4.1.11
- UniProt
- B0VJ11
- Ligands
- NAP, CL, SO4
- Pockets
- 6 · best druggability 0.78
Structure
x-ray diffraction · 2 distinct chains · 34% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 3,5-diaminohexanoate dehydrogenase (EC 1.4.1.11) | protein | 351 | 34% helix, 24% strand | B0VJ11 |
| B | 3,5-diaminohexanoate dehydrogenase (EC 1.4.1.11) | protein | 355 | 34% helix, 25% strand | B0VJ11 |
Ligands and binding sites
- NAP · Nadp nicotinamide-adenine-dinucleotide phosphate · ligand · chains A, B
- CL · Chloride ion · ion · 2 copies · chains A
- SO4 · Sulfate ion · ion · 2 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 3 copies · chains A, B
- GOL · Glycerol · additive · 3 copies · chains A, B
- PEG · Di(hydroxyethyl)ether · additive · 2 copies · chains A, B
- PGE · Triethylene glycol · additive · 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, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 484 | 0.78 | 0.85 | 59 | NAP |
| 2 | 698 | 0.73 | 0.79 | 71 | GOL, CL |
| 3 | 181 | 0.45 | 0.75 | 39 | GOL |
| 4 | 144 | 0.45 | 0.76 | 35 | PGE |
| 5 | 157 | 0.44 | 0.75 | 31 | PEG |
Interfaces
1 interface between chains.
- A–B · 2236 Ų buried · 31 hydrogen bonds · protein-protein
Compared structures
- 7DL0 · The mutant E310G/A314Y of 3,5-DAHDHcca complex with NADPH · 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 B0VJ11
- Elsewhere: RCSB PDB 7DL0 · PDBe 7DL0 · UniProt B0VJ11
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