Research workbench
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)-4-chlorobenzoic 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
- 6PF8
- Type
- protein
- Length
- 2,529 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, OE7, MTX
- Pockets
- 20 · best druggability 0.80
Structure
x-ray diffraction · 2 distinct chains · 29% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, D, E | Bifunctional dihydrofolate reductase-thymidylate synthase | protein | 506 | 29% helix, 25% strand | A0A0S4TER9 |
| C | Bifunctional dihydrofolate reductase-thymidylate synthase | protein | 505 | 29% 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
- OE7 · 2-({4-[(2-amino-4-oxo-4,7-dihydro-3H-pyrrolo[2,3-d]pyrimidin-5-yl)methyl]benzene-1-carbonyl}amino)-4-chlorobenzoic acid · ligand · 5 copies · chains A, B, C, D, E
- MTX · Methotrexate · ligand · 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, 19 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 356 | 0.80 | 0.89 | 44 | UFP, OE7 |
| 2 | 677 | 0.79 | 0.84 | 69 | NDP, MTX |
| 3 | 687 | 0.79 | 0.83 | 75 | MTX |
| 4 | 385 | 0.77 | 0.87 | 43 | UFP, OE7 |
| 5 | 396 | 0.77 | 0.86 | 43 | UFP, OE7 |
Interfaces
7 interfaces between chains.
- C–D · 4249 Ų buried · 69 hydrogen bonds · protein-protein
- A–B · 4242 Ų buried · 72 hydrogen bonds · protein-protein
- B–D · 238 Ų buried · 10 hydrogen bonds · protein-protein
- C–E · 237 Ų buried · 9 hydrogen bonds · protein-protein
- A–C · 235 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 6PF8 · 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 6PF8 · PDBe 6PF8 · UniProt A0A0S4TER9
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