MolNFT v1 · #160258 · protein
Crystal structure of ts-DHFR from cryptosporidium hominis in complex with NADPH, fdump and 2-(4-((2-amino-4-oxo-4,7-dihydro-3H-PYRROLO[2, 3-D]PYRIMIDIN-5-YL)METHYL)BENZAMIDO)BENZOIC acid
6PF7 · Bifunctional dihydrofolate reductase-thymidylate synthase: “Crystal structure of ts-DHFR from cryptosporidium hominis in complex with NADPH, fdump and…”. X-ray diffraction, 5 ligands (NDP, UFP, OG7), 20 pockets (best druggability…
- PDB
- 6PF7
- Type
- protein
- Length
- 2,537 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Bifunctional dihydrofolate reductase-thymidylate synthase
- UniProt
- A0A0S4TER9
- Ligands
- NDP, UFP, OG7, MTX, SO4
- Pockets
- 20 · best druggability 0.79
Structure
x-ray diffraction · 2 distinct chains · 29% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, D | Bifunctional dihydrofolate reductase-thymidylate synthase | protein | 507 | 29% helix, 25% strand | A0A0S4TER9 |
| C, E | Bifunctional dihydrofolate reductase-thymidylate synthase | protein | 508 | 28% helix, 25% 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
- OG7 · 2-({4-[(2-amino-4-oxo-4,7-dihydro-1H-pyrrolo[2,3-d]pyrimidin-5-yl)methyl]benzene-1-carbonyl}amino) benzoic 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 · 4 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, 18 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1031 | 0.79 | 0.81 | 88 | NDP, MTX |
| 2 | 772 | 0.78 | 0.82 | 68 | NDP, MTX |
| 3 | 617 | 0.78 | 0.84 | 66 | UFP, OG7 |
| 4 | 393 | 0.78 | 0.87 | 47 | UFP, OG7 |
| 5 | 779 | 0.78 | 0.82 | 71 | NDP, MTX |
Interfaces
7 interfaces between chains.
- C–D · 4341 Ų buried · 65 hydrogen bonds · protein-protein
- A–B · 4295 Ų buried · 68 hydrogen bonds · protein-protein
- D–E · 235 Ų buried · 4 hydrogen bonds · protein-protein
- A–C · 221 Ų buried · 5 hydrogen bonds · protein-protein
- B–D · 217 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 6PF7 · 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 6PF7 · PDBe 6PF7 · UniProt A0A0S4TER9
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