Research workbench
Structure of ALDH4A1 complexed with trans-4-hydroxy-L-proline
Analyse Structure of ALDH4A1 complexed with trans-4-hydroxy-L-proline in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7MER
- Type
- protein
- Length
- 1,067 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
- HYP, SO4
- Pockets
- 10 · best druggability 0.80
Structure
x-ray diffraction · 2 distinct chains · 41% 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 | 532 | 41% helix, 22% strand | Q8CHT0 |
| B | Delta-1-pyrroline-5-carboxylate dehydrogenase, mitochondrial (EC 1.2.1.88) | protein | 535 | 41% helix, 22% strand | Q8CHT0 |
Ligands and binding sites
- HYP · 4-hydroxyproline · ligand · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 2 copies · chains A, B
- 1PE · Pentaethylene glycol · additive · 2 copies · chains A, B
- PEG · Di(hydroxyethyl)ether · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 161 | 0.80 | 0.96 | 38 | empty |
| 2 | 352 | 0.77 | 0.87 | 58 | empty |
| 3 | 502 | 0.74 | 0.83 | 67 | HYP |
| 4 | 505 | 0.74 | 0.82 | 68 | HYP |
| 5 | 374 | 0.60 | 0.76 | 39 | empty |
Interfaces
1 interface between chains.
- A–B · 4623 Ų buried · 84 hydrogen bonds · protein-protein
Compared structures
- 7MER · Structure of ALDH4A1 complexed with trans-4-Hydroxy-L-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 B 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 7MER · PDBe 7MER · UniProt Q8CHT0
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