Research workbench
Crystal structure of yeast ALDH4A1 complexed with NAD+
Analyse Crystal structure of yeast ALDH4A1 complexed with NAD+ in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4OE4
- Type
- protein
- Length
- 960 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Delta-1-pyrroline-5-carboxylate dehydrogenase, mitochondrial
- EC
- 1.2.1.88
- UniProt
- P07275
- Ligands
- NAD
- Pockets
- 9 · best druggability 0.77
Structure
x-ray diffraction · 2 distinct chains · 46% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Delta-1-pyrroline-5-carboxylate dehydrogenase, mitochondrial (EC 1.2.1.88) | protein | 479 | 46% helix, 23% strand | P07275 |
| B | Delta-1-pyrroline-5-carboxylate dehydrogenase, mitochondrial (EC 1.2.1.88) | protein | 481 | 46% helix, 23% strand | P07275 |
Ligands and binding sites
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 841 | 0.77 | 0.80 | 72 | empty |
| 2 | 361 | 0.62 | 0.78 | 39 | NAD |
| 3 | 366 | 0.62 | 0.77 | 40 | NAD |
| 4 | 260 | 0.56 | 0.77 | 29 | empty |
| 5 | 180 | 0.48 | 0.76 | 23 | empty |
Interfaces
1 interface between chains.
- A–B · 2079 Ų buried · 45 hydrogen bonds · protein-protein
Compared structures
- 4OE4 · Crystal Structure of Yeast ALDH4A1 Complexed with NAD+ · the same entry in another collection · chain A against A, TM-score 1.00
- P07275 · AlphaFold monomer V2.0 prediction for delta-1-pyrroline-5-carboxylate dehydrogenase… · a predicted model of the same protein · chain A against A, TM-score 0.98
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 P07275
- Elsewhere: RCSB PDB 4OE4 · PDBe 4OE4 · UniProt P07275
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