Research workbench
Structure of bifunctional tcdhfr-ts in complex with mtx
Analyse Structure of bifunctional tcdhfr-ts in complex with mtx in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3CL9
- Type
- protein
- Length
- 505 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Bifunctional dihydrofolate reductase-thymidylate synthase (DHFR-ts)
- EC
- 1.5.1.3, 2.1.1.45
- UniProt
- Q27793
- Ligands
- NAP, MTX, UMP, CL, SO4
- Pockets
- 8 · best druggability 0.70
Structure
x-ray diffraction · 1 distinct chain · 30% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Bifunctional dihydrofolate reductase-thymidylate synthase (DHFR-ts) (EC 1.5.1.3, 2.1.1.45) | protein | 505 | 30% helix, 26% strand | Q27793 |
Ligands and binding sites
- NAP · Nadp nicotinamide-adenine-dinucleotide phosphate · ligand · chains A
- MTX · Methotrexate · ligand · chains A
- UMP · 2'-deoxyuridine 5'-monophosphate · ligand · chains A
- CL · Chloride ion · ion · 3 copies · chains A
- SO4 · Sulfate ion · ion · 2 copies · chains A
- EDO · 1,2-ethanediol · additive · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 380 | 0.70 | 0.82 | 41 | NAP, MTX |
| 2 | 444 | 0.63 | 0.77 | 37 | UMP |
| 3 | 156 | 0.57 | 0.82 | 22 | empty |
| 4 | 231 | 0.57 | 0.78 | 29 | empty |
| 5 | 194 | 0.52 | 0.78 | 29 | empty |
Compared structures
- 3CL9 · Structure of bifunctional TcDHFR-TS in complex with MTX · the same entry in another collection · chain A against A, TM-score 1.00
- Q27793 · AlphaFold monomer V2.0 prediction for bifunctional dihydrofolate reductase-thymidylate… · a predicted model of the same protein · chain A against A, TM-score 0.94
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 3CL9 · PDBe 3CL9 · UniProt Q27793
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