Research workbench
Structure of phosphonoacetaldehyde dehydrogenase in the apo state
Analyse Structure of phosphonoacetaldehyde dehydrogenase in the apo state in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4I3T
- Type
- protein
- Length
- 3,792 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
- PO4
- Pockets
- 20 · best druggability 0.81
Structure
x-ray diffraction · 1 distinct chain · 40% helix, 23% 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 | 474 | 40% helix, 23% strand | Q92UV7 |
Ligands and binding sites
- PO4 · Phosphate ion · ion · 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 | 1106 | 0.81 | 0.83 | 103 | empty |
| 2 | 409 | 0.81 | 0.89 | 39 | empty |
| 3 | 497 | 0.75 | 0.84 | 60 | empty |
| 4 | 225 | 0.74 | 0.89 | 43 | PO4 |
| 5 | 565 | 0.70 | 0.79 | 70 | PO4 |
Interfaces
13 interfaces between chains.
- C–E · 2681 Ų buried · 44 hydrogen bonds · protein-protein
- A–F · 2681 Ų buried · 46 hydrogen bonds · protein-protein
- B–E · 1107 Ų buried · 17 hydrogen bonds · protein-protein
- B–C · 704 Ų buried · 10 hydrogen bonds · protein-protein
- A–B · 261 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 4I3T · Structure of phosphonoacetaldehyde dehydrogenase in the apo state · 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 4I3T · PDBe 4I3T · UniProt Q92UV7
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