Research workbench
Structure of zm ALDH2-3 (RF2C) in complex with NAD
Analyse Structure of zm ALDH2-3 (RF2C) in complex with NAD in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4PXL
- Type
- protein
- Length
- 972 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cytosolic aldehyde dehydrogenase RF2C
- UniProt
- Q8S531
- Ligands
- NAD, NA, CA
- Pockets
- 6 · best druggability 0.84
Structure
x-ray diffraction · 1 distinct chain · 41% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Cytosolic aldehyde dehydrogenase RF2C | protein | 486 | 41% helix, 21% strand | Q8S531 |
Ligands and binding sites
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 2 copies · chains A, B
- NA · Sodium ion · metal · 2 copies · chains A, B
- CA · Calcium ion · metal
- EDO · 1,2-ethanediol · additive · 9 copies · chains A, B
- PEG · Di(hydroxyethyl)ether · additive · 4 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1060 | 0.84 | 0.85 | 106 | empty |
| 2 | 613 | 0.75 | 0.82 | 80 | NAD |
| 3 | 427 | 0.71 | 0.82 | 50 | PEG |
| 4 | 346 | 0.65 | 0.80 | 41 | NAD, CA |
| 5 | 63 | 0.36 | 0.78 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 2604 Ų buried · 38 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 modified (oxidation).
Compared structures
- 4PXL · Structure of Zm ALDH2-3 (RF2C) in complex with NAD · the same entry in another collection · 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 Q8S531
- Elsewhere: RCSB PDB 4PXL · PDBe 4PXL · UniProt Q8S531
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