Research workbench
Crystal structure of escherichia COLI dihydrofolate reductase in complex with trimethoprim and NADPH
Analyse Crystal structure of escherichia COLI dihydrofolate reductase in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7MYM
- Type
- protein
- Length
- 474 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Dihydrofolate reductase
- EC
- 1.5.1.3
- UniProt
- P0ABQ5
- Ligands
- NAP, TOP, ARG, SO4
- Pockets
- 6 · best druggability 0.71
Structure
x-ray diffraction · 1 distinct chain · 23% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, B | Dihydrofolate reductase (EC 1.5.1.3) | protein | 158 | 23% helix, 31% strand | P0ABQ5 |
Ligands and binding sites
- NAP · Nadp nicotinamide-adenine-dinucleotide phosphate · ligand · 3 copies · chains A, C, B
- TOP · Trimethoprim · ligand · 3 copies · chains A, C, B
- ARG · Arginine · ligand · 2 copies · chains A, C
- SO4 · Sulfate ion · ion · 4 copies · chains A, C, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 355 | 0.71 | 0.83 | 43 | NAP, TOP |
| 2 | 353 | 0.70 | 0.83 | 40 | NAP, TOP, SO4 |
| 3 | 327 | 0.70 | 0.83 | 40 | NAP, TOP |
| 4 | 337 | 0.60 | 0.77 | 35 | empty |
| 5 | 157 | 0.55 | 0.81 | 20 | empty |
Interfaces
2 interfaces between chains.
- A–C · 601 Ų buried · 7 hydrogen bonds · protein-protein
- A–B · 232 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 7MYM · Crystal structure of Escherichia coli dihydrofolate reductase in complex with… · the same entry in another collection · chain A against A, TM-score 1.00
- P0ABQ5 · AlphaFold monomer V2.0 prediction for dihydrofolate reductase (P0ABQ5) · 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 P0ABQ5
- Elsewhere: RCSB PDB 7MYM · PDBe 7MYM · UniProt P0ABQ5
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