Research workbench
Leishmania major pteridine reductase 1 in complex with NADP and trimethoprim
Analyse Leishmania major pteridine reductase 1 in complex with NADP and trimethoprim in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2BFM
- Type
- protein
- Length
- 1,042 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
- NDP, TOP
- Pockets
- 11 · best druggability 0.82
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 | 266 | 47% helix, 15% strand | Q01782 |
| B | Pteridine reductase 1 (EC 1.5.1.33) | protein | 266 | 47% helix, 15% strand | Q01782 |
| C | Pteridine reductase 1 (EC 1.5.1.33) | protein | 254 | 48% helix, 16% strand | Q01782 |
| D | Pteridine reductase 1 (EC 1.5.1.33) | protein | 256 | 46% helix, 17% strand | Q01782 |
Ligands and binding sites
- NDP · Nadph dihydro-nicotinamide-adenine-dinucleotide phosphate · ligand · 4 copies · chains A, B, C, D
- TOP · Trimethoprim · ligand · 2 copies · chains A, D, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1146 | 0.82 | 0.84 | 86 | empty |
| 2 | 703 | 0.73 | 0.79 | 62 | NDP, TOP |
| 3 | 612 | 0.72 | 0.80 | 48 | NDP, TOP |
| 4 | 541 | 0.71 | 0.80 | 43 | NDP |
| 5 | 529 | 0.71 | 0.80 | 46 | NDP |
Interfaces
6 interfaces between chains.
- A–B · 1979 Ų buried · 10 hydrogen bonds · protein-protein
- C–D · 1922 Ų buried · 10 hydrogen bonds · protein-protein
- A–C · 1625 Ų buried · 9 hydrogen bonds · protein-protein
- B–D · 1624 Ų buried · 10 hydrogen bonds · protein-protein
- B–C · 652 Ų buried · 13 hydrogen bonds · protein-protein
Compared structures
- 2BFM · Leishmania major pteridine reductase 1 in complex with NADP and trimethoprim · 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 2BFM · PDBe 2BFM · UniProt Q01782
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