MolNFT v1 · #67678 · protein
Trypanosoma cruzi dihydrofolate reductase-thymidylate synthase complexed with cycloguanil
3IRM · Bifunctional dihydrofolate reductase-thymidylate synthase: “Trypanosoma cruzi dihydrofolate reductase-thymidylate synthase complexed with cycloguanil”. X-ray diffraction, 2 ligands (1CY, PO4), 20 pockets (best druggability 0.82).…
- PDB
- 3IRM
- Type
- protein
- Length
- 2,068 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Bifunctional dihydrofolate reductase-thymidylate synthase
- EC
- 1.5.1.3, 2.1.1.45
- UniProt
- Q27793
- Ligands
- 1CY, PO4
- Pockets
- 20 · best druggability 0.82
Structure
x-ray diffraction · 4 distinct chains · 30% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Bifunctional dihydrofolate reductase-thymidylate synthase (EC 1.5.1.3, 2.1.1.45) | protein | 520 | 31% helix, 26% strand | Q27793 |
| B | Bifunctional dihydrofolate reductase-thymidylate synthase (EC 1.5.1.3, 2.1.1.45) | protein | 519 | 29% helix, 26% strand | Q27793 |
| C | Bifunctional dihydrofolate reductase-thymidylate synthase (EC 1.5.1.3, 2.1.1.45) | protein | 516 | 30% helix, 26% strand | Q27793 |
| D | Bifunctional dihydrofolate reductase-thymidylate synthase (EC 1.5.1.3, 2.1.1.45) | protein | 513 | 31% helix, 26% strand | Q27793 |
Ligands and binding sites
- 1CY · 1-(4-chlorophenyl)-6,6-dimethyl-1,6-dihydro-1,3,5-triazine-2,4-diamine · ligand · 4 copies · chains A, B, C, D
- PO4 · Phosphate ion · ion · 8 copies · chains A, B, C, D
- ACT · Acetate ion · additive · 8 copies · chains A, C, B, 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 | 1187 | 0.82 | 0.83 | 104 | empty |
| 2 | 1180 | 0.82 | 0.83 | 108 | empty |
| 3 | 1175 | 0.81 | 0.83 | 103 | ACT |
| 4 | 668 | 0.76 | 0.81 | 68 | empty |
| 5 | 364 | 0.73 | 0.84 | 35 | empty |
Interfaces
6 interfaces between chains.
- C–D · 2076 Ų buried · 27 hydrogen bonds · protein-protein
- A–B · 2055 Ų buried · 29 hydrogen bonds · protein-protein
- A–C · 1125 Ų buried · 18 hydrogen bonds · protein-protein
- B–D · 1041 Ų buried · 18 hydrogen bonds · protein-protein
- B–C · 765 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 3IRM · Trypanosoma cruzi Dihydrofolate Reductase-Thymidylate Synthase COMPLEXED WITH Cycloguanil · the same entry in another collection · chain D against D, TM-score 1.00
- Q27793 · AlphaFold monomer V2.0 prediction for bifunctional dihydrofolate reductase-thymidylate… · a predicted model of the same protein · chain D against A, TM-score 0.98
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 Q27793
- Elsewhere: RCSB PDB 3IRM · PDBe 3IRM · UniProt Q27793
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