MolNFT v1 · #185484 · protein
The crystal structure of leishmania major pteridine reductase 1 in complex with substrate folic acid
7PXX: “The crystal structure of leishmania major pteridine reductase 1 in complex with substrate folic acid”. X-ray diffraction, 2 ligands (FOL, NDP), 13 pockets (best druggability 0.84). MolNFT v1 #185484 on GenesisL1: 3D structure…
- PDB
- 7PXX
- Type
- protein
- Length
- 1,034 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Pteridine reductase 1
- EC
- 1.5.1.33
- UniProt
- Q01782
- Ligands
- FOL, NDP
- Pockets
- 13 · best druggability 0.84
Structure
x-ray diffraction · 4 distinct chains · 47% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Pteridine reductase 1 (EC 1.5.1.33) | protein | 264 | 47% helix, 16% strand | Q01782 |
| B | Pteridine reductase 1 (EC 1.5.1.33) | protein | 265 | 48% helix, 16% strand | Q01782 |
| C | Pteridine reductase 1 (EC 1.5.1.33) | protein | 253 | 47% helix, 17% strand | Q01782 |
| D | Pteridine reductase 1 (EC 1.5.1.33) | protein | 252 | 47% helix, 17% strand | Q01782 |
Ligands and binding sites
- FOL · Folic acid · ligand · 4 copies · chains A, B, C, D
- NDP · Nadph dihydro-nicotinamide-adenine-dinucleotide phosphate · ligand · 4 copies · chains A, B, C, D
- GOL · Glycerol · additive · 4 copies · chains B, A, D
- PGE · Triethylene glycol · additive · 2 copies · chains A, C, B, D
- PEG · Di(hydroxyethyl)ether · additive · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1078 | 0.84 | 0.85 | 76 | empty |
| 2 | 569 | 0.73 | 0.81 | 48 | FOL, NDP |
| 3 | 572 | 0.73 | 0.81 | 46 | FOL, NDP |
| 4 | 505 | 0.70 | 0.80 | 43 | FOL, NDP |
| 5 | 466 | 0.70 | 0.80 | 43 | FOL, NDP |
Interfaces
6 interfaces between chains.
- C–D · 1727 Ų buried · 11 hydrogen bonds · protein-protein
- A–B · 1720 Ų buried · 11 hydrogen bonds · protein-protein
- B–D · 1627 Ų buried · 11 hydrogen bonds · protein-protein
- A–C · 1617 Ų buried · 13 hydrogen bonds · protein-protein
- A–D · 666 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 modified (oxidation).
Compared structures
- 7PXX · The crystal structure of Leishmania major Pteridine Reductase 1 in complex with substrate… · the same entry in another collection · chain D against D, TM-score 1.00
- Q01782 · AlphaFold monomer V2.0 prediction for pteridine reductase 1 (Q01782) · 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 Q01782
- Elsewhere: RCSB PDB 7PXX · PDBe 7PXX · UniProt Q01782
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