MolNFT v1 · #182614 · protein
Crystal structure of escherichia COLI dihydrofolate reductase in complex with trimethoprim and NADPH
7MYM: “Crystal structure of escherichia COLI dihydrofolate reductase in complex with trimethoprim and NADPH”. X-ray diffraction, 4 ligands (NAP, TOP, ARG), 6 pockets (best druggability 0.71). MolNFT v1 #182614 on GenesisL1: 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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