MolNFT v1 · #94681 · protein
Structure of phosphonoacetaldehyde dehydrogenase in complex with phosphonoacetate and cofactor NAD+
4I3X · Aldehyde dehydrogenase (NAD+): “Structure of phosphonoacetaldehyde dehydrogenase in complex with phosphonoacetate and cofactor NAD+”. X-ray diffraction, 2 ligands (NAD, PAE), 20 pockets (best druggability 0.86). MolNFT v1 #94681 on…
- PDB
- 4I3X
- Type
- protein
- Length
- 3,803 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
- NAD, PAE
- Pockets
- 20 · best druggability 0.86
Structure
x-ray diffraction · 3 distinct chains · 40% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D, E, F, H | Aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) | protein | 476 | 40% helix, 22% strand | Q92UV7 |
| B, G | Aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) | protein | 474 | 40% helix, 23% strand | Q92UV7 |
| C | Aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) | protein | 475 | 40% helix, 21% strand | Q92UV7 |
Ligands and binding sites
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 8 copies · chains A, B, C, D, E, F, G, H
- PAE · Phosphonoacetic acid · ligand · 8 copies · chains A, B, C, D, E, F, G, H
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 | 632 | 0.86 | 0.91 | 77 | empty |
| 2 | 381 | 0.82 | 0.91 | 45 | empty |
| 3 | 931 | 0.77 | 0.80 | 79 | empty |
| 4 | 374 | 0.76 | 0.86 | 55 | empty |
| 5 | 262 | 0.76 | 0.89 | 41 | empty |
Interfaces
13 interfaces between chains.
- A–B · 2644 Ų buried · 39 hydrogen bonds · protein-protein
- D–H · 2626 Ų buried · 39 hydrogen bonds · protein-protein
- B–H · 1143 Ų buried · 17 hydrogen bonds · protein-protein
- A–D · 1120 Ų buried · 16 hydrogen bonds · protein-protein
- A–H · 758 Ų buried · 13 hydrogen bonds · protein-protein
Compared structures
- 4I3X · Structure of phosphonoacetaldehyde dehydrogenase in complex with phosphonoacetate and… · 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 C 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 4I3X · PDBe 4I3X · UniProt Q92UV7
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