Research workbench
Structure of phosphonoacetaldehyde dehydrogenase in complex with phosphonoacetaldehyde and cofactor NAD+
Analyse Structure of phosphonoacetaldehyde dehydrogenase in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4I3V
- 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
- POA, NAD
- Pockets
- 20 · best druggability 0.82
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
- POA · Phosphonoacetaldehyde · 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 | 377 | 0.82 | 0.91 | 43 | empty |
| 2 | 1119 | 0.81 | 0.82 | 106 | empty |
| 3 | 316 | 0.81 | 0.92 | 42 | empty |
| 4 | 575 | 0.80 | 0.86 | 57 | empty |
| 5 | 498 | 0.80 | 0.87 | 51 | empty |
Interfaces
16 interfaces between chains.
- B–F · 2675 Ų buried · 36 hydrogen bonds · protein-protein
- D–E · 2664 Ų buried · 38 hydrogen bonds · protein-protein
- A–C · 2654 Ų buried · 35 hydrogen bonds · protein-protein
- G–H · 2562 Ų buried · 33 hydrogen bonds · protein-protein
- A–D · 1166 Ų buried · 16 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 covalent (covalent ligand).
Compared structures
- 4I3V · Structure of phosphonoacetaldehyde dehydrogenase in complex with phosphonoacetaldehyde… · 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 0.99
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 4I3V · PDBe 4I3V · UniProt Q92UV7
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