Research workbench
Crystal structure of a 'humanized' E. COLI dihydrofolate reductase
Analyse Crystal structure of a 'humanized' E. 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
- 4GH8
- Type
- protein
- Length
- 324 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
- MTX, NDP, CA
- Pockets
- 4 · best druggability 0.72
Structure
x-ray diffraction · 1 distinct chain · 25% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B, A | Dihydrofolate reductase (EC 1.5.1.3) | protein | 162 | 25% helix, 31% strand | P0ABQ4 |
Ligands and binding sites
- MTX · Methotrexate · ligand · 2 copies · chains B, A
- NDP · Nadph dihydro-nicotinamide-adenine-dinucleotide phosphate · ligand · 2 copies · chains B, A
- CA · Calcium ion · metal · 3 copies · chains B, A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 392 | 0.72 | 0.83 | 46 | MTX, NDP |
| 2 | 341 | 0.71 | 0.83 | 36 | MTX |
| 3 | 52 | 0.33 | 0.78 | 18 | empty |
| 4 | 51 | 0.33 | 0.78 | 14 | empty |
Interfaces
1 interface between chains.
- B–A · 473 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 4GH8 · Crystal structure of a 'humanized' E. coli dihydrofolate reductase · 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 A against A, TM-score 0.96
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 4GH8 · PDBe 4GH8 · UniProt P0ABQ4
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