Research workbench
Crystal structure of daua in complex with NADP+
Analyse Crystal structure of daua in complex with NADP+ in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6POP
- Type
- protein
- Length
- 2,850 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Aldehyde dehydrogenase
- Ligands
- NAP, MG
- Pockets
- 20 · best druggability 0.83
Structure
x-ray diffraction · 1 distinct chain · 41% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F | Aldehyde dehydrogenase | protein | 475 | 41% helix, 23% strand | — |
Ligands and binding sites
- NAP · Nadp nicotinamide-adenine-dinucleotide phosphate · ligand · 6 copies · chains A, B, C, D, E, F
- MG · Magnesium ion · metal · 2 copies · chains B, C
- EDO · 1,2-ethanediol · additive · 14 copies · chains A, E, B, C, D, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 15 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 940 | 0.83 | 0.84 | 114 | NAP, MG, EDO |
| 2 | 709 | 0.81 | 0.85 | 77 | EDO |
| 3 | 766 | 0.81 | 0.84 | 89 | NAP, EDO, MG |
| 4 | 722 | 0.80 | 0.84 | 65 | EDO |
| 5 | 440 | 0.79 | 0.87 | 57 | EDO |
Interfaces
10 interfaces between chains.
- A–E · 2776 Ų buried · 50 hydrogen bonds · protein-protein
- C–D · 2681 Ų buried · 46 hydrogen bonds · protein-protein
- B–F · 2680 Ų buried · 45 hydrogen bonds · protein-protein
- C–E · 274 Ų buried · 1 hydrogen bond · protein-protein
- A–B · 269 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 6POP · Crystal structure of DauA in complex with NADP+ · 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
- Elsewhere: RCSB PDB 6POP · PDBe 6POP
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