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Isomorphous crystal structures of escherichia COLI dihydrofolate reductase complexed with folate, 5- deazafolate and 5,10-dideazatetrahydrofolate: mechanistic implications
Analyse Isomorphous crystal structures of escherichia COLI dihydrofolate reductase… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1DYJ
- Type
- protein
- Length
- 318 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Dihydrofolate reductase
- EC
- 1.5.1.3
- UniProt
- P0ABQ4
- Ligands
- DDF, CA, CL
- Pockets
- 3 · best druggability 0.77
Structure
x-ray diffraction · 1 distinct chain · 25% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Dihydrofolate reductase (EC 1.5.1.3) | protein | 159 | 25% helix, 31% strand | P0ABQ4 |
Ligands and binding sites
- DDF · 5,10-dideazatetrahydrofolic acid · ligand · 2 copies · chains A, B
- CA · Calcium ion · metal · chains B
- CL · Chloride ion · ion · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 531 | 0.77 | 0.84 | 45 | CL, DDF |
| 2 | 623 | 0.73 | 0.80 | 47 | CL, DDF |
| 3 | 67 | 0.31 | 0.75 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 567 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 1DYJ · Isomorphous crystal structures of escherichia COLI dihydrofolate reductase complexed with… · the same entry in another collection · chain A against A, TM-score 1.00
- P0ABQ4 · AlphaFold monomer V2.0 prediction for dihydrofolate reductase (P0ABQ4) · a predicted model of the same protein · chain B against A, TM-score 0.98
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 P0ABQ4
- Elsewhere: RCSB PDB 1DYJ · PDBe 1DYJ · UniProt P0ABQ4
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