MolNFT v1 · #182035 · protein
Structure of ALDH4A1 complexed with trans-4-hydroxy-D-proline
7MES · Delta-1-pyrroline-5-carboxylate dehydrogenase, mitochondrial: “Structure of ALDH4A1 complexed with trans-4-hydroxy-D-proline”. X-ray diffraction, 2 ligands (UY7, NAD), 12 pockets (best druggability 0.76). MolNFT v1 #182035 on…
- PDB
- 7MES
- Type
- protein
- Length
- 1,050 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
- Q8CHT0
- Ligands
- UY7, NAD
- Pockets
- 12 · best druggability 0.76
Structure
x-ray diffraction · 2 distinct chains · 42% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Delta-1-pyrroline-5-carboxylate dehydrogenase, mitochondrial (EC 1.2.1.88) | protein | 523 | 42% helix, 22% strand | Q8CHT0 |
| B | Delta-1-pyrroline-5-carboxylate dehydrogenase, mitochondrial (EC 1.2.1.88) | protein | 527 | 42% helix, 22% strand | Q8CHT0 |
Ligands and binding sites
- UY7 · (4S)-4-hydroxy-D-proline · ligand · 4 copies · chains A, B
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 2 copies · chains A, B
- PEG · Di(hydroxyethyl)ether · additive · 3 copies · chains A, B
- 1PE · Pentaethylene glycol · additive · 2 copies · chains A, B
- PG4 · Tetraethylene glycol · additive · chains A
- PGE · Triethylene glycol · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 360 | 0.76 | 0.86 | 59 | empty |
| 2 | 93 | 0.73 | 0.95 | 19 | empty |
| 3 | 356 | 0.70 | 0.82 | 55 | UY7 |
| 4 | 374 | 0.68 | 0.81 | 61 | UY7 |
| 5 | 453 | 0.63 | 0.76 | 61 | NAD, PEG |
Interfaces
1 interface between chains.
- A–B · 3470 Ų buried · 65 hydrogen bonds · protein-protein
Compared structures
- 7MES · Structure of ALDH4A1 complexed with trans-4-Hydroxy-D-proline · the same entry in another collection · chain A against A, TM-score 1.00
- Q8CHT0 · 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 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 Q8CHT0
- Elsewhere: RCSB PDB 7MES · PDBe 7MES · UniProt Q8CHT0
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