Research workbench
Crystal structure of human pyrroline-5-carboxylate reductase complexed with NADP
Analyse Crystal structure of human pyrroline-5-carboxylate reductase complexed with NADP in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2GRA
- Type
- protein
- Length
- 1,384 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Pyrroline-5-carboxylate reductase 1
- EC
- 1.5.1.2
- UniProt
- P32322
- Ligands
- NAP, GLU
- Pockets
- 20 · best druggability 0.72
Structure
x-ray diffraction · 2 distinct chains · 50% helix, 9% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, D, E | Pyrroline-5-carboxylate reductase 1 (EC 1.5.1.2) | protein | 277 | 53% helix, 12% strand | P32322 |
| B | Pyrroline-5-carboxylate reductase 1 (EC 1.5.1.2) | protein | 276 | 47% helix, 7% strand | P32322 |
Ligands and binding sites
- NAP · Nadp nicotinamide-adenine-dinucleotide phosphate · ligand · 5 copies · chains A, B, C, D, E
- GLU · Glutamic acid · ligand · 5 copies · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 63 | 0.72 | 0.97 | 21 | empty |
| 2 | 61 | 0.64 | 0.93 | 25 | empty |
| 3 | 459 | 0.58 | 0.73 | 49 | empty |
| 4 | 353 | 0.54 | 0.73 | 40 | empty |
| 5 | 165 | 0.53 | 0.79 | 37 | empty |
Interfaces
5 interfaces between chains.
- C–D · 424 Ų buried · 8 hydrogen bonds · protein-protein
- B–E · 388 Ų buried · 6 hydrogen bonds · protein-protein
- A–C · 386 Ų buried · 10 hydrogen bonds · protein-protein
- A–E · 377 Ų buried · 3 hydrogen bonds · protein-protein
- B–D · 362 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 5 disulfide (disulfide).
Compared structures
- 2GRA · crystal structure of Human Pyrroline-5-carboxylate Reductase complexed with nadp · the same entry in another collection · chain E against E, TM-score 1.00
- P32322 · AlphaFold monomer V2.0 prediction for pyrroline-5-carboxylate reductase 1, mitochondrial… · 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 P32322
- Elsewhere: RCSB PDB 2GRA · PDBe 2GRA · UniProt P32322
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