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Co-crystal structure of dihydrofolate reductase-thymidylate synthase from babesia bovis with dump, raltitrexed and NADP
Analyse Co-crystal structure of dihydrofolate reductase-thymidylate synthase from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3NRR
- Type
- protein
- Length
- 1,004 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Dihydrofolate reductase-thymidylate synthase
- EC
- 2.1.1.45
- UniProt
- A7ASX7
- Ligands
- D16, NAP, UMP, CL, PO4
- Pockets
- 12 · best druggability 0.77
Structure
x-ray diffraction · 2 distinct chains · 30% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Dihydrofolate reductase-thymidylate synthase (EC 2.1.1.45) | protein | 503 | 30% helix, 25% strand | A7ASX7 |
| B | Dihydrofolate reductase-thymidylate synthase (EC 2.1.1.45) | protein | 501 | 30% helix, 25% strand | A7ASX7 |
Ligands and binding sites
- D16 · Tomudex · ligand · 4 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
- CL · Chloride ion · ion · 2 copies · chains A
- PO4 · Phosphate ion · ion · chains B
- EDO · 1,2-ethanediol · additive · 13 copies · chains A, B
- GOL · Glycerol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 354 | 0.77 | 0.87 | 45 | UMP, D16 |
| 2 | 329 | 0.76 | 0.87 | 41 | UMP, D16 |
| 3 | 513 | 0.76 | 0.83 | 48 | NAP, D16 |
| 4 | 459 | 0.74 | 0.83 | 50 | NAP, D16 |
| 5 | 215 | 0.52 | 0.76 | 25 | EDO |
Interfaces
1 interface between chains.
- A–B · 3290 Ų buried · 42 hydrogen bonds · protein-protein
Compared structures
- 3NRR · Co-crystal structure of dihydrofolate reductase-thymidylate synthase from Babesia bovis… · the same entry in another collection · chain B against B, 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 A7ASX7
- Elsewhere: RCSB PDB 3NRR · PDBe 3NRR · UniProt A7ASX7
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