Research workbench
Staphylococcus aureus S1:DHFR in complex with trimethoprim
Analyse Staphylococcus aureus S1:DHFR in complex with trimethoprim in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2W9S
- Type
- protein
- Length
- 942 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Dihydrofolate reductase type 1 from TN4003
- EC
- 1.5.1.3
- UniProt
- P13955
- Ligands
- TOP, NDP
- Pockets
- 9 · best druggability 0.82
Structure
x-ray diffraction · 1 distinct chain · 20% helix, 35% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F | Dihydrofolate reductase type 1 from TN4003 (EC 1.5.1.3) | protein | 157 | 20% helix, 35% strand | P13955 |
Ligands and binding sites
- TOP · Trimethoprim · ligand · 6 copies · chains A, B, C, D, E, F
- NDP · Nadph dihydro-nicotinamide-adenine-dinucleotide phosphate · ligand · 3 copies · chains A, B, C
- GOL · Glycerol · additive · 6 copies · chains A, D, B, F, C, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 747 | 0.82 | 0.86 | 53 | TOP |
| 2 | 896 | 0.81 | 0.83 | 105 | NDP, TOP |
| 3 | 844 | 0.81 | 0.84 | 66 | TOP |
| 4 | 1047 | 0.80 | 0.81 | 74 | GOL, TOP |
| 5 | 329 | 0.70 | 0.83 | 39 | NDP, TOP |
Interfaces
8 interfaces between chains.
- A–D · 756 Ų buried · 10 hydrogen bonds · protein-protein
- B–F · 736 Ų buried · 9 hydrogen bonds · protein-protein
- C–D · 667 Ų buried · 10 hydrogen bonds · protein-protein
- B–E · 662 Ų buried · 9 hydrogen bonds · protein-protein
- A–F · 646 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 2W9S · Staphylococcus aureus S1:DHFR in complex with trimethoprim · the same entry in another collection · chain A against A, TM-score 1.00
- P13955 · AlphaFold monomer V2.0 prediction for dihydrofolate reductase type 1 from TN4003 (P13955) · a predicted model of the same protein · chain C 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 P13955
- Elsewhere: RCSB PDB 2W9S · PDBe 2W9S · UniProt P13955
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