Research workbench
Structure of phosphonoacetaldehyde dehydrogenase in complex with phosphonoacetaldehyde
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
- 4I3U
- 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
- Pockets
- 20 · best druggability 0.82
Structure
x-ray diffraction · 1 distinct chain · 41% 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 | 41% helix, 22% strand | Q92UV7 |
Ligands and binding sites
- POA · Phosphonoacetaldehyde · 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 | 422 | 0.82 | 0.90 | 49 | empty |
| 2 | 358 | 0.82 | 0.91 | 40 | empty |
| 3 | 1172 | 0.78 | 0.80 | 108 | empty |
| 4 | 168 | 0.72 | 0.90 | 31 | empty |
| 5 | 170 | 0.71 | 0.90 | 27 | empty |
Interfaces
13 interfaces between chains.
- F–H · 2680 Ų buried · 40 hydrogen bonds · protein-protein
- A–D · 2671 Ų buried · 39 hydrogen bonds · protein-protein
- D–H · 1142 Ų buried · 18 hydrogen bonds · protein-protein
- A–F · 1135 Ų buried · 17 hydrogen bonds · protein-protein
- A–H · 698 Ų buried · 15 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 covalent (covalent ligand).
Compared structures
- 4I3U · 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 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 4I3U · PDBe 4I3U · UniProt Q92UV7
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