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Crystal structure of plasmodium falciparum pyrroline carboxylate reductase (MAL13P1.284) with NADP bound
Analyse Crystal structure of plasmodium falciparum pyrroline carboxylate reductase… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2RCY
- Type
- protein
- Length
- 1,268 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Pyrroline carboxylate reductase
- EC
- 1.5.1.2
- UniProt
- Q8IDC6
- Ligands
- NAP, MG
- Pockets
- 12 · best druggability 0.73
Structure
x-ray diffraction · 5 distinct chains · 56% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Pyrroline carboxylate reductase (EC 1.5.1.2) | protein | 262 | 56% helix, 14% strand | Q8IDC6 |
| B | Pyrroline carboxylate reductase (EC 1.5.1.2) | protein | 253 | 58% helix, 13% strand | Q8IDC6 |
| C | Pyrroline carboxylate reductase (EC 1.5.1.2) | protein | 261 | 56% helix, 14% strand | Q8IDC6 |
| D | Pyrroline carboxylate reductase (EC 1.5.1.2) | protein | 248 | 53% helix, 13% strand | Q8IDC6 |
| E | Pyrroline carboxylate reductase (EC 1.5.1.2) | protein | 244 | 56% helix, 12% strand | Q8IDC6 |
Ligands and binding sites
- NAP · Nadp nicotinamide-adenine-dinucleotide phosphate · ligand · 5 copies · chains A, E, B, C, D
- MG · Magnesium ion · metal · 4 copies · chains A, E, B, C, D
- GOL · Glycerol · additive · 2 copies · chains A, E, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 589 | 0.73 | 0.81 | 72 | NAP |
| 2 | 507 | 0.71 | 0.80 | 62 | NAP |
| 3 | 344 | 0.71 | 0.83 | 47 | NAP |
| 4 | 1113 | 0.70 | 0.74 | 101 | NAP |
| 5 | 235 | 0.70 | 0.86 | 36 | NAP |
Interfaces
8 interfaces between chains.
- A–E · 4821 Ų buried · 29 hydrogen bonds · protein-protein
- B–C · 4805 Ų buried · 28 hydrogen bonds · protein-protein
- A–B · 784 Ų buried · 8 hydrogen bonds · protein-protein
- A–C · 423 Ų buried · 4 hydrogen bonds · protein-protein
- B–E · 413 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 47 modified (engineered).
Compared structures
- 2RCY · Crystal structure of Plasmodium falciparum pyrroline carboxylate reductase (MAL13P1.284)… · the same entry in another collection · 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 Q8IDC6
- Elsewhere: RCSB PDB 2RCY · PDBe 2RCY · UniProt Q8IDC6
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