Research workbench
Crystal structure of wild type plasmodium falciparum DHFR-ts complexed with BT1, NADPH, and dump
Analyse Crystal structure of wild type plasmodium falciparum DHFR-ts complexed with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6A2K
- Type
- protein
- Length
- 1,070 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Bifunctional dihydrofolate reductase-thymidylate synthase
- UniProt
- A7UD81
- Ligands
- 9QO, NAP, UMP
- Pockets
- 14 · best druggability 0.74
Structure
x-ray diffraction · 2 distinct chains · 31% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Bifunctional dihydrofolate reductase-thymidylate synthase | protein | 543 | 32% helix, 25% strand | A7UD81 |
| B | Bifunctional dihydrofolate reductase-thymidylate synthase | protein | 527 | 30% helix, 26% strand | A7UD81 |
Ligands and binding sites
- 9QO · 5-(3-{3-[(2,4-diamino-6-ethylpyrimidin-5-yl) oxy]propoxy}phenyl)-6-ethylpyrimidine-2,4-diamine · ligand · 2 copies · chains A, B
- NAP · Nadp nicotinamide-adenine-dinucleotide phosphate · ligand · 2 copies · chains A, B
- UMP · 2'-deoxyuridine 5'-monophosphate · ligand · 2 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 | 504 | 0.74 | 0.82 | 49 | 9QO, NAP |
| 2 | 500 | 0.74 | 0.82 | 50 | 9QO, NAP |
| 3 | 657 | 0.70 | 0.77 | 66 | UMP |
| 4 | 575 | 0.69 | 0.78 | 55 | UMP |
| 5 | 307 | 0.55 | 0.75 | 35 | empty |
Interfaces
1 interface between chains.
- A–B · 4211 Ų buried · 51 hydrogen bonds · protein-protein
Compared structures
- 6A2K · Crystal structure of wild type Plasmodium falciparum DHFR-TS complexed with BT1, NADPH… · 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 A7UD81
- Elsewhere: RCSB PDB 6A2K · PDBe 6A2K · UniProt A7UD81
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