Research workbench
Structure of human ALDH4A1 crystallized in space group P21
Analyse Structure of human ALDH4A1 crystallized in space group P21 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4OE5
- Type
- protein
- Length
- 2,054 residues
- Chains
- 4
- 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
- P30038
- Ligands
- MG
- Pockets
- 18 · best druggability 0.87
Structure
x-ray diffraction · 4 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 | 505 | 42% helix, 22% strand | P30038 |
| B | Delta-1-pyrroline-5-carboxylate dehydrogenase, mitochondrial (EC 1.2.1.88) | protein | 522 | 42% helix, 21% strand | P30038 |
| C | Delta-1-pyrroline-5-carboxylate dehydrogenase, mitochondrial (EC 1.2.1.88) | protein | 520 | 41% helix, 21% strand | P30038 |
| D | Delta-1-pyrroline-5-carboxylate dehydrogenase, mitochondrial (EC 1.2.1.88) | protein | 507 | 42% helix, 22% strand | P30038 |
Ligands and binding sites
- MG · Magnesium ion · metal · chains B
- 1PE · Pentaethylene glycol · additive · 3 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
18 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1088 | 0.87 | 0.89 | 119 | MG |
| 2 | 380 | 0.82 | 0.91 | 52 | empty |
| 3 | 398 | 0.81 | 0.89 | 46 | empty |
| 4 | 931 | 0.73 | 0.76 | 93 | empty |
| 5 | 323 | 0.72 | 0.85 | 53 | empty |
Interfaces
6 interfaces between chains.
- A–B · 2199 Ų buried · 30 hydrogen bonds · protein-protein
- C–D · 2110 Ų buried · 30 hydrogen bonds · protein-protein
- B–D · 258 Ų buried · 6 hydrogen bonds · protein-protein
- A–C · 138 Ų buried · 4 hydrogen bonds · protein-protein
- A–D · 136 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- P30038 · AlphaFold monomer V2.0 prediction for delta-1-pyrroline-5-carboxylate dehydrogenase… · a predicted model of the same protein · chain D 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 P30038
- Elsewhere: RCSB PDB 4OE5 · PDBe 4OE5 · UniProt P30038
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