Research workbench
Crystal structure of DFRA1 dihydrofolate reductase in complex with trimethoprim
Analyse Crystal structure of DFRA1 dihydrofolate reductase 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
- 7MYL
- Type
- protein
- Length
- 940 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Dihydrofolate reductase
- EC
- 1.5.1.3
- UniProt
- A4GRC7
- Ligands
- TOP
- Pockets
- 9 · best druggability 0.79
Structure
x-ray diffraction · 4 distinct chains · 20% helix, 35% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, F | Dihydrofolate reductase (EC 1.5.1.3) | protein | 157 | 18% helix, 36% strand | A4GRC7 |
| B | Dihydrofolate reductase (EC 1.5.1.3) | protein | 158 | 19% helix, 35% strand | A4GRC7 |
| C | Dihydrofolate reductase (EC 1.5.1.3) | protein | 156 | 22% helix, 36% strand | A4GRC7 |
| D, E | Dihydrofolate reductase (EC 1.5.1.3) | protein | 156 | 20% helix, 34% strand | A4GRC7 |
Ligands and binding sites
- TOP · Trimethoprim · ligand · 6 copies · chains A, B, E, C, D, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 781 | 0.79 | 0.82 | 80 | TOP |
| 2 | 683 | 0.71 | 0.78 | 71 | TOP |
| 3 | 536 | 0.70 | 0.80 | 70 | TOP |
| 4 | 253 | 0.59 | 0.79 | 33 | TOP |
| 5 | 153 | 0.58 | 0.83 | 23 | empty |
Interfaces
9 interfaces between chains.
- E–F · 1078 Ų buried · 14 hydrogen bonds · protein-protein
- B–C · 1042 Ų buried · 10 hydrogen bonds · protein-protein
- A–D · 717 Ų buried · 8 hydrogen bonds · protein-protein
- B–E · 532 Ų buried · 7 hydrogen bonds · protein-protein
- C–E · 199 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 7MYL · Crystal structure of DfrA1 dihydrofolate reductase in complex with TRIMETHOPRIM · the same entry in another collection · chain A 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 A4GRC7
- Elsewhere: RCSB PDB 7MYL · PDBe 7MYL · UniProt A4GRC7
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