Research workbench
The structure of 3,5-dahdhcca complex with NADPH
Analyse The structure of 3,5-dahdhcca complex with NADPH in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7DL3
- Type
- protein
- Length
- 1,407 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, CL
- Pockets
- 12 · best druggability 0.72
Structure
x-ray diffraction · 2 distinct chains · 36% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 3,5-diaminohexanoate dehydrogenase (EC 1.4.1.11) | protein | 354 | 36% helix, 25% strand | B0VJ11 |
| B, C, D | 3,5-diaminohexanoate dehydrogenase (EC 1.4.1.11) | protein | 351 | 36% helix, 26% strand | B0VJ11 |
Ligands and binding sites
- NAP · Nadp nicotinamide-adenine-dinucleotide phosphate · ligand · 2 copies · chains A, C
- CL · Chloride ion · ion · 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, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 799 | 0.72 | 0.78 | 85 | NAP |
| 2 | 711 | 0.71 | 0.77 | 68 | empty |
| 3 | 703 | 0.70 | 0.77 | 79 | empty |
| 4 | 627 | 0.68 | 0.77 | 82 | empty |
| 5 | 612 | 0.68 | 0.77 | 65 | NAP |
Interfaces
4 interfaces between chains.
- B–D · 2099 Ų buried · 25 hydrogen bonds · protein-protein
- A–C · 2088 Ų buried · 27 hydrogen bonds · protein-protein
- B–C · 607 Ų buried · 7 hydrogen bonds · protein-protein
- A–D · 605 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 7DL3 · The 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 7DL3 · PDBe 7DL3 · UniProt B0VJ11
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