MolNFT v1 · #176389 · protein
The mutant E310G/G323S structure of 3,5-dahdhcca complex with NADPH
7DL1 · 3,5-diaminohexanoate dehydrogenase: “The mutant E310G/G323S structure of 3,5-dahdhcca complex with NADPH”. X-ray diffraction, 1 ligand (NAP), 12 pockets (best druggability 0.72). MolNFT v1 #176389 on GenesisL1: 3D structure, binding…
- PDB
- 7DL1
- Type
- protein
- Length
- 1,404 residues
- Chains
- 4
- 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
- Pockets
- 12 · best druggability 0.72
Structure
x-ray diffraction · 1 distinct chain · 35% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | 3,5-diaminohexanoate dehydrogenase (EC 1.4.1.11) | protein | 351 | 35% helix, 25% strand | B0VJ11 |
Ligands and binding sites
- NAP · Nadp nicotinamide-adenine-dinucleotide phosphate · ligand · 2 copies · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 819 | 0.72 | 0.77 | 93 | NAP |
| 2 | 792 | 0.71 | 0.77 | 93 | empty |
| 3 | 680 | 0.71 | 0.78 | 74 | empty |
| 4 | 703 | 0.69 | 0.77 | 74 | NAP |
| 5 | 682 | 0.69 | 0.77 | 72 | empty |
Interfaces
4 interfaces between chains.
- A–C · 2008 Ų buried · 25 hydrogen bonds · protein-protein
- B–D · 1983 Ų buried · 26 hydrogen bonds · protein-protein
- A–D · 605 Ų buried · 6 hydrogen bonds · protein-protein
- B–C · 605 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 7DL1 · The mutant E310G/G323S structure 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 7DL1 · PDBe 7DL1 · UniProt B0VJ11
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