Research workbench
Structure of bifunctional tcdhfr-ts in complex with tmq
Analyse Structure of bifunctional tcdhfr-ts in complex with tmq in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3CLB
- Type
- protein
- Length
- 2,037 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DHFR-ts
- EC
- 1.5.1.3, 2.1.1.45
- UniProt
- Q27793
- 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 | DHFR-ts (EC 1.5.1.3, 2.1.1.45) | protein | 510 | 28% helix, 27% strand | Q27793 |
| B | DHFR-ts (EC 1.5.1.3, 2.1.1.45) | protein | 508 | 27% helix, 26% strand | Q27793 |
| C | DHFR-ts (EC 1.5.1.3, 2.1.1.45) | protein | 510 | 27% helix, 26% strand | Q27793 |
| D | DHFR-ts (EC 1.5.1.3, 2.1.1.45) | protein | 509 | 28% helix, 27% strand | Q27793 |
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 · 4 copies · chains A, D, B, C
- EDO · 1,2-ethanediol · additive · 6 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 | 1034 | 0.83 | 0.84 | 103 | EDO |
| 2 | 1046 | 0.83 | 0.84 | 97 | empty |
| 3 | 740 | 0.80 | 0.84 | 83 | empty |
| 4 | 419 | 0.80 | 0.88 | 53 | empty |
| 5 | 436 | 0.79 | 0.88 | 55 | EDO |
Interfaces
6 interfaces between chains.
- B–C · 2247 Ų buried · 36 hydrogen bonds · protein-protein
- A–D · 2223 Ų buried · 32 hydrogen bonds · protein-protein
- A–B · 1073 Ų buried · 15 hydrogen bonds · protein-protein
- C–D · 1052 Ų buried · 20 hydrogen bonds · protein-protein
- B–D · 894 Ų buried · 14 hydrogen bonds · protein-protein
Compared structures
- 3CLB · Structure of bifunctional TcDHFR-TS in complex with TMQ · 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 C 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 3CLB · PDBe 3CLB · UniProt Q27793
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