Research workbench
Crystal structure of mus musculus 1-pyrroline-5-carboxylate dehydrogenase cryoprotected in proline
Analyse Crystal structure of mus musculus 1-pyrroline-5-carboxylate dehydrogenase… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4E3X
- Type
- protein
- Length
- 1,089 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Delta-1-pyrroline-5-carboxylate dehydrogenase, mitochondrial
- EC
- 1.5.1.12
- UniProt
- Q8CHT0
- Ligands
- PRO, 16P
- Pockets
- 8 · best druggability 0.78
Structure
x-ray diffraction · 2 distinct chains · 40% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Delta-1-pyrroline-5-carboxylate dehydrogenase, mitochondrial (EC 1.5.1.12) | protein | 543 | 40% helix, 20% strand | Q8CHT0 |
| B | Delta-1-pyrroline-5-carboxylate dehydrogenase, mitochondrial (EC 1.5.1.12) | protein | 546 | 40% helix, 21% strand | Q8CHT0 |
Ligands and binding sites
- PRO · Proline · ligand · 7 copies · chains A, B
- 16P · 3,6,9,12,15,18-hexaoxaicosane · ligand · chains A
- PGE · Triethylene glycol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 993 | 0.78 | 0.80 | 107 | PRO |
| 2 | 135 | 0.78 | 0.96 | 34 | empty |
| 3 | 877 | 0.77 | 0.80 | 104 | PRO |
| 4 | 435 | 0.77 | 0.85 | 64 | empty |
| 5 | 236 | 0.56 | 0.78 | 41 | PRO |
Interfaces
1 interface between chains.
- A–B · 4866 Ų buried · 88 hydrogen bonds · protein-protein
Compared structures
- 4E3X · Crystal Structure of Mus musculus 1-pyrroline-5-carboxylate dehydrogenase cryoprotected… · the same entry in another collection · chain B against B, 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 4E3X · PDBe 4E3X · UniProt Q8CHT0
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