MolNFT v1 · #65927 · protein
Structures of dihydrofolate reductase-thymidylate synthase of trypanosoma cruzi in the folate-free state and in complex with two antifolate drugs, trimetrexate and methotrexate
3HBB: “Structures of dihydrofolate reductase-thymidylate synthase of trypanosoma cruzi in the folate-free state and…”. X-ray diffraction, 3 ligands (NAP, TMQ, SO4), 20 pockets (best druggability 0.83). MolNFT v1 #65927 on GenesisL1: 3D…
- PDB
- 3HBB
- Type
- protein
- Length
- 2,032 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
- NAP, TMQ, SO4
- Pockets
- 20 · best druggability 0.83
Structure
x-ray diffraction · 4 distinct chains · 28% 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 | 510 | 29% helix, 27% strand | Q8T5T8 |
| B | Dihydrofolate reductase-thymidylate synthase (EC 1.5.1.3, 2.1.1.45) | protein | 505 | 28% helix, 26% strand | Q8T5T8 |
| C | Dihydrofolate reductase-thymidylate synthase (EC 1.5.1.3, 2.1.1.45) | protein | 510 | 28% helix, 26% strand | Q8T5T8 |
| D | Dihydrofolate reductase-thymidylate synthase (EC 1.5.1.3, 2.1.1.45) | protein | 507 | 28% helix, 27% strand | Q8T5T8 |
Ligands and binding sites
- NAP · Nadp nicotinamide-adenine-dinucleotide phosphate · ligand · 4 copies · chains A, B, C, D
- TMQ · Trimetrexate · ligand · 4 copies · chains A, B, C, D
- SO4 · Sulfate ion · ion · 28 copies · chains A, D, B, C
- EDO · 1,2-ethanediol · additive · 12 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 | 1035 | 0.83 | 0.84 | 100 | SO4 |
| 2 | 1035 | 0.83 | 0.84 | 103 | EDO |
| 3 | 689 | 0.83 | 0.87 | 85 | EDO |
| 4 | 449 | 0.80 | 0.88 | 57 | EDO |
| 5 | 423 | 0.75 | 0.85 | 57 | empty |
Interfaces
6 interfaces between chains.
- B–C · 2246 Ų buried · 35 hydrogen bonds · protein-protein
- A–D · 2211 Ų buried · 29 hydrogen bonds · protein-protein
- C–D · 1044 Ų buried · 23 hydrogen bonds · protein-protein
- A–B · 971 Ų buried · 15 hydrogen bonds · protein-protein
- B–D · 896 Ų buried · 15 hydrogen bonds · protein-protein
Compared structures
- 3HBB · Structures of dihydrofolate reductase-thymidylate synthase of Trypanosoma cruzi in the… · 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 3HBB · PDBe 3HBB · UniProt Q8T5T8
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