MolNFT v1 · #94680 · protein
Structure of phosphonoacetaldehyde dehydrogenase in complex with gylceraldehyde-3-phosphate and cofactor NAD+
4I3W · Aldehyde dehydrogenase (NAD+): “Structure of phosphonoacetaldehyde dehydrogenase in complex with gylceraldehyde-3-phosphate and cofactor NAD+”. X-ray diffraction, 2 ligands (G3H, NAD), 20 pockets (best druggability 0.89). MolNFT v1…
- PDB
- 4I3W
- Type
- protein
- Length
- 3,784 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Aldehyde dehydrogenase (NAD+)
- EC
- 1.2.1.3
- UniProt
- Q92UV7
- Ligands
- G3H, NAD
- Pockets
- 20 · best druggability 0.89
Structure
x-ray diffraction · 1 distinct chain · 40% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F, G, H | Aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) | protein | 473 | 40% helix, 22% strand | Q92UV7 |
Ligands and binding sites
- G3H · Glyceraldehyde-3-phosphate · ligand · 8 copies · chains A, B, C, D, E, F, G, H
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 7 copies · chains A, B, C, D, E, F, G
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 943 | 0.89 | 0.91 | 109 | empty |
| 2 | 1013 | 0.84 | 0.85 | 101 | empty |
| 3 | 1057 | 0.84 | 0.85 | 106 | empty |
| 4 | 437 | 0.83 | 0.91 | 64 | empty |
| 5 | 326 | 0.81 | 0.92 | 34 | empty |
Interfaces
14 interfaces between chains.
- B–C · 2668 Ų buried · 35 hydrogen bonds · protein-protein
- G–H · 2661 Ų buried · 37 hydrogen bonds · protein-protein
- A–F · 2659 Ų buried · 35 hydrogen bonds · protein-protein
- D–E · 2658 Ų buried · 37 hydrogen bonds · protein-protein
- C–E · 1136 Ų buried · 16 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 covalent (covalent ligand).
Compared structures
- 4I3W · Structure of phosphonoacetaldehyde dehydrogenase in complex with… · the same entry in another collection · chain H against H, TM-score 1.00
- Q92UV7 · AlphaFold monomer V2.0 prediction for phosphonoacetaldehyde dehydrogenase (Q92UV7) · a predicted model of the same protein · 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 Q92UV7
- Elsewhere: RCSB PDB 4I3W · PDBe 4I3W · UniProt Q92UV7
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