Research workbench
Crystal structure of TS-DHFR from Cryptosporidium hominis in complex with NADPH, FdUMP and 2-(2-(4-((2-amino-4-oxo-4,7-dihydro-3H-pyrrolo[2,3-d]pyrimidin-5-yl)methyl)benzamido)phenyl)acetic acid.
Analyse Crystal structure of TS-DHFR from Cryptosporidium hominis in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6PF9
- Type
- protein
- Length
- 2,529 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.89
- Source
- Cryptosporidium hominis
- Molecule
- Bifunctional dihydrofolate reductase-thymidylate synthase
- UniProt
- A0A0S4TER9
- Ligands
- NDP, UFP, OF7, MTX, SO4
- Pockets
- 20 · best druggability 0.79
Structure
x-ray diffraction · resolution 2.89 · 2 distinct chains · 28% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Bifunctional dihydrofolate reductase-thymidylate synthase | protein | 506 | 28% helix, 25% strand | A0A0S4TER9 |
| E | Bifunctional dihydrofolate reductase-thymidylate synthase | protein | 505 | 28% helix, 26% strand | A0A0S4TER9 |
Ligands and binding sites
- NDP · Nadph dihydro-nicotinamide-adenine-dinucleotide phosphate · ligand · 5 copies · chains A, B, C, D, E
- UFP · 5-fluoro-2'-deoxyuridine-5'-monophosphate · ligand · 5 copies · chains A, B, C, D, E
- OF7 · [2-({4-[(2-amino-4-oxo-4,7-dihydro-3H-pyrrolo[2,3-d]pyrimidin-5-yl)methyl]benzene-1-carbonyl}amino) phenyl]acetic acid · ligand · 5 copies · chains A, B, C, D, E
- MTX · Methotrexate · ligand · 5 copies · chains A, B, C, D, E
- SO4 · Sulfate ion · ion · 5 copies · chains A, B, C, D, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 15 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1078 | 0.79 | 0.81 | 99 | NDP, MTX |
| 2 | 402 | 0.78 | 0.87 | 45 | UFP, OF7 |
| 3 | 424 | 0.78 | 0.86 | 47 | UFP, OF7 |
| 4 | 850 | 0.77 | 0.81 | 74 | NDP, MTX |
| 5 | 445 | 0.76 | 0.84 | 47 | UFP, OF7 |
Interfaces
6 interfaces between chains.
- B–C · 4283 Ų buried · 68 hydrogen bonds · protein-protein
- C–E · 412 Ų buried · 3 hydrogen bonds · protein-protein
- A–B · 229 Ų buried · 6 hydrogen bonds · protein-protein
- C–D · 225 Ų buried · 5 hydrogen bonds · protein-protein
- B–D · 157 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 6PF9 · Crystal structure of ts-DHFR from cryptosporidium hominis in complex with NADPH, fdump… · 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 A0A0S4TER9
- Elsewhere: RCSB PDB 6PF9 · PDBe 6PF9 · UniProt A0A0S4TER9
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