Research workbench
Staphylococcus aureus dihydrofolate reductase complexed with NADPH and 6-ethyl-5-(3-(4-methoxybiphenyl-3-YL)PROP-1-YNYL)PYRIMIDINE-2,4- diamine (UCP120J)
Analyse Staphylococcus aureus dihydrofolate reductase complexed with NADPH and… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3SH2
- 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, 5DR
- Pockets
- 5 · best druggability 0.70
Structure
x-ray diffraction · 1 distinct chain · 19% helix, 36% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Dihydrofolate reductase (EC 1.5.1.3) | protein | 157 | 19% helix, 36% strand | P0A017 |
Ligands and binding sites
- NDP · Nadph dihydro-nicotinamide-adenine-dinucleotide phosphate · ligand · 2 copies · chains A, B
- 5DR · 6-ethyl-5-[3-(4-methoxybiphenyl-3-yl)prop-1-yn-1-yl]pyrimidine-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
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 394 | 0.70 | 0.81 | 40 | NDP, 5DR |
| 2 | 364 | 0.68 | 0.81 | 41 | NDP, 5DR |
| 3 | 88 | 0.38 | 0.76 | 16 | empty |
| 4 | 71 | 0.32 | 0.75 | 15 | empty |
| 5 | 64 | 0.29 | 0.74 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 473 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 3SH2 · Staphylococcus aureus 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 A 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 3SH2 · PDBe 3SH2 · UniProt P0A017
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