MolNFT v1 · #82009 · protein
Crystal structure of human 1-pyrroline-5-carboxylate dehydrogenase mutant S352L
3V9I · Delta-1-pyrroline-5-carboxylate dehydrogenase, mitochondrial: “Crystal structure of human 1-pyrroline-5-carboxylate dehydrogenase mutant S352L”. X-ray diffraction, 16 pockets (best druggability 0.77). MolNFT v1 #82009 on GenesisL1…
- PDB
- 3V9I
- Type
- protein
- Length
- 1,982 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
- 16 · best druggability 0.77
Structure
x-ray diffraction · 4 distinct chains · 42% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Delta-1-pyrroline-5-carboxylate dehydrogenase, mitochondrial (EC 1.5.1.12) | protein | 506 | 43% helix, 23% strand | P30038 |
| B | Delta-1-pyrroline-5-carboxylate dehydrogenase, mitochondrial (EC 1.5.1.12) | protein | 502 | 42% helix, 24% strand | P30038 |
| C | Delta-1-pyrroline-5-carboxylate dehydrogenase, mitochondrial (EC 1.5.1.12) | protein | 492 | 43% helix, 23% strand | P30038 |
| D | Delta-1-pyrroline-5-carboxylate dehydrogenase, mitochondrial (EC 1.5.1.12) | protein | 482 | 42% helix, 22% strand | P30038 |
Pockets
16 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 779 | 0.77 | 0.81 | 88 | empty |
| 2 | 576 | 0.74 | 0.82 | 95 | empty |
| 3 | 698 | 0.74 | 0.80 | 77 | empty |
| 4 | 342 | 0.72 | 0.84 | 60 | empty |
| 5 | 425 | 0.65 | 0.78 | 53 | empty |
Interfaces
4 interfaces between chains.
- A–B · 3294 Ų buried · 47 hydrogen bonds · protein-protein
- C–D · 2285 Ų buried · 32 hydrogen bonds · protein-protein
- B–D · 608 Ų buried · 17 hydrogen bonds · protein-protein
- A–C · 534 Ų buried · 12 hydrogen bonds · protein-protein
Compared structures
- 3V9I · Crystal structure of human 1-pyrroline-5-carboxylate dehydrogenase mutant S352L · 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 0.99
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 3V9I · PDBe 3V9I · UniProt P30038
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