MolNFT v1 · #69214 · protein
Crystal structure of T. cruzi DHFR-ts with 3 high affinity DHFR inhibitors: DQ1 inhibitor complex
3KJS · Dihydrofolate reductase-thymidylate synthase: “Crystal structure of T. cruzi DHFR-ts with 3 high affinity DHFR inhibitors: DQ1 inhibitor complex”. X-ray diffraction, 3 ligands (DQ1, NAP, SO4), 20 pockets (best druggability 0.84).…
- PDB
- 3KJS
- Type
- protein
- Length
- 2,010 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Dihydrofolate reductase-thymidylate synthase
- EC
- 1.5.1.3, 2.1.1.45
- UniProt
- Q8T5T8
- Ligands
- DQ1, NAP, SO4
- Pockets
- 20 · best druggability 0.84
Structure
x-ray diffraction · 4 distinct chains · 29% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Dihydrofolate reductase-thymidylate synthase (EC 1.5.1.3, 2.1.1.45) | protein | 500 | 27% helix, 28% strand | Q8T5T8 |
| B | Dihydrofolate reductase-thymidylate synthase (EC 1.5.1.3, 2.1.1.45) | protein | 499 | 29% helix, 27% strand | Q8T5T8 |
| C | Dihydrofolate reductase-thymidylate synthase (EC 1.5.1.3, 2.1.1.45) | protein | 507 | 29% helix, 26% strand | Q8T5T8 |
| D | Dihydrofolate reductase-thymidylate synthase (EC 1.5.1.3, 2.1.1.45) | protein | 504 | 30% helix, 27% strand | Q8T5T8 |
Ligands and binding sites
- DQ1 · ethyl 4-(5-{[(2,4-diaminoquinazolin-6-yl)methyl]amino}-2-methoxyphenoxy)butanoate · ligand · 4 copies · chains A, B, C, D
- NAP · Nadp nicotinamide-adenine-dinucleotide phosphate · ligand · 4 copies · chains A, B, C, D
- SO4 · Sulfate ion · ion · 8 copies · chains A, B, C, D
- EDO · 1,2-ethanediol · additive · 13 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 993 | 0.84 | 0.85 | 99 | empty |
| 2 | 645 | 0.83 | 0.88 | 83 | empty |
| 3 | 642 | 0.83 | 0.88 | 86 | empty |
| 4 | 354 | 0.77 | 0.88 | 44 | empty |
| 5 | 689 | 0.74 | 0.80 | 59 | empty |
Interfaces
6 interfaces between chains.
- B–C · 2269 Ų buried · 37 hydrogen bonds · protein-protein
- A–D · 2258 Ų buried · 31 hydrogen bonds · protein-protein
- C–D · 1074 Ų buried · 22 hydrogen bonds · protein-protein
- B–D · 1011 Ų buried · 17 hydrogen bonds · protein-protein
- A–C · 989 Ų buried · 14 hydrogen bonds · protein-protein
Compared structures
- 3KJS · Crystal Structure of T. cruzi DHFR-TS with 3 high affinity DHFR inhibitors: DQ1 inhibitor… · 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 Q8T5T8
- Elsewhere: RCSB PDB 3KJS · PDBe 3KJS · UniProt Q8T5T8
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