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Co-crystal structure of dihydrofolate REDUCTASE/THYMIDYLATE synthase from babesia bovis with dump, pemetrexed and NADP
Analyse Co-crystal structure of dihydrofolate REDUCTASE/THYMIDYLATE synthase from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3K2H
- Type
- protein
- Length
- 1,006 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Dihydrofolate REDUCTASE/THYMIDYLATE synthase
- EC
- 2.1.1.45
- UniProt
- A7ASX7
- Ligands
- LYA, UMP, NAP
- Pockets
- 14 · best druggability 0.77
Structure
x-ray diffraction · 1 distinct chain · 29% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Dihydrofolate REDUCTASE/THYMIDYLATE synthase (EC 2.1.1.45) | protein | 503 | 29% helix, 25% strand | A7ASX7 |
Ligands and binding sites
- LYA · 2-{4-[2-(2-amino-4-oxo-4,7-dihydro-3H-pyrrolo[2,3-d]pyrimidin-5-yl)-ethyl]-benzoylamino}-pentanedioic acid · ligand · 4 copies · chains A, B
- UMP · 2'-deoxyuridine 5'-monophosphate · ligand · 2 copies · chains A, B
- NAP · Nadp nicotinamide-adenine-dinucleotide phosphate · ligand · 2 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 5 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 467 | 0.77 | 0.85 | 50 | LYA, NAP |
| 2 | 335 | 0.76 | 0.87 | 43 | UMP, LYA |
| 3 | 446 | 0.76 | 0.84 | 52 | LYA, NAP |
| 4 | 322 | 0.76 | 0.87 | 44 | UMP, LYA |
| 5 | 214 | 0.52 | 0.77 | 24 | empty |
Interfaces
1 interface between chains.
- A–B · 3298 Ų buried · 41 hydrogen bonds · protein-protein
Compared structures
- 3K2H · Co-crystal structure of dihydrofolate reductase/thymidylate synthase from Babesia bovis… · 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 A7ASX7
- Elsewhere: RCSB PDB 3K2H · PDBe 3K2H · UniProt A7ASX7
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