Research workbench
Staphylococcus aureus V31Y, F92I mutant dihydrofolate reductase complexed with NADPH and 5-[(3S)-3-(5-methoxy-2',6'-dimethylbiphenyl- 3-YL)BUT-1-yn-1-yl]-6-methylpyrimidine-2,4-diamine
Analyse Staphylococcus aureus V31Y, F92I mutant dihydrofolate reductase complexed with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3LG4
- Type
- protein
- Length
- 314 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Dihydrofolate reductase
- EC
- 1.5.1.3
- UniProt
- P0A017
- Ligands
- NDP, 52V
- Pockets
- 4 · best druggability 0.72
Structure
x-ray diffraction · 1 distinct chain · 20% helix, 34% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Dihydrofolate reductase (EC 1.5.1.3) | protein | 157 | 20% helix, 34% strand | P0A017 |
Ligands and binding sites
- NDP · Nadph dihydro-nicotinamide-adenine-dinucleotide phosphate · ligand · 2 copies · chains A, B
- 52V · 5-[(3S)-3-(5-methoxy-2',6'-dimethylbiphenyl-3-yl)but-1-yn-1-yl]-6-methylpyrimidine-2,4-diamine · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 389 | 0.72 | 0.83 | 48 | NDP, 52V |
| 2 | 408 | 0.71 | 0.82 | 54 | NDP, 52V |
| 3 | 100 | 0.37 | 0.75 | 21 | empty |
| 4 | 78 | 0.33 | 0.75 | 13 | empty |
Interfaces
1 interface between chains.
- A–B · 458 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 3LG4 · Staphylococcus aureus V31Y, F92I mutant dihydrofolate reductase complexed with NADPH and… · the same entry in another collection · chain A against A, TM-score 1.00
- P0A017 · AlphaFold monomer V2.0 prediction for dihydrofolate reductase (P0A017) · a predicted model of the same protein · chain B 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 P0A017
- Elsewhere: RCSB PDB 3LG4 · PDBe 3LG4 · UniProt P0A017
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