Research workbench
Crystal structure of human 1-pyrroline-5-carboxylate dehydrogenase
Analyse Crystal structure of human 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
- 3V9G
- Type
- protein
- Length
- 2,162 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Delta-1-pyrroline-5-carboxylate dehydrogenase, mitochondrial
- EC
- 1.5.1.12
- UniProt
- P30038
- Pockets
- 20 · best druggability 0.79
Structure
x-ray diffraction · 2 distinct chains · 41% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Delta-1-pyrroline-5-carboxylate dehydrogenase, mitochondrial (EC 1.5.1.12) | protein | 541 | 41% helix, 23% strand | P30038 |
| C, D | Delta-1-pyrroline-5-carboxylate dehydrogenase, mitochondrial (EC 1.5.1.12) | protein | 540 | 41% helix, 23% strand | P30038 |
Pockets
20 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 134 | 0.79 | 0.97 | 30 | empty |
| 2 | 120 | 0.76 | 0.95 | 32 | empty |
| 3 | 493 | 0.76 | 0.84 | 67 | empty |
| 4 | 440 | 0.76 | 0.85 | 61 | empty |
| 5 | 504 | 0.76 | 0.84 | 66 | empty |
Interfaces
4 interfaces between chains.
- A–B · 4535 Ų buried · 75 hydrogen bonds · protein-protein
- C–D · 4531 Ų buried · 70 hydrogen bonds · protein-protein
- B–D · 670 Ų buried · 19 hydrogen bonds · protein-protein
- A–C · 571 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
- 3V9G · Crystal structure of human 1-pyrroline-5-carboxylate dehydrogenase · the same entry in another collection · chain D against D, TM-score 1.00
- P30038 · AlphaFold monomer V2.0 prediction for delta-1-pyrroline-5-carboxylate dehydrogenase… · a predicted model of the same protein · chain C 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 P30038
- Elsewhere: RCSB PDB 3V9G · PDBe 3V9G · UniProt P30038
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