MolNFT v1 · #64521 · protein
Crystal structure of thermus thermophilus trmfo in complex with glutathione
3G5S · Methylenetetrahydrofolate--tRNA-(uracil-5-)…: “Crystal structure of thermus thermophilus trmfo in complex with glutathione”. X-ray diffraction, 3 ligands (FAD, GSH, MG), 5 pockets (best druggability 0.74). MolNFT v1 #64521 on…
- PDB
- 3G5S
- Type
- protein
- Length
- 424 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Methylenetetrahydrofolate--tRNA-(uracil-5-)- methyltransferase trmfo
- EC
- 2.1.1.74
- UniProt
- Q5SID2
- Ligands
- FAD, GSH, MG
- Pockets
- 5 · best druggability 0.74
Structure
x-ray diffraction · 1 distinct chain · 37% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Methylenetetrahydrofolate--tRNA-(uracil-5-)- methyltransferase trmfo (EC 2.1.1.74) | protein | 424 | 37% helix, 19% strand | Q5SID2 |
Ligands and binding sites
- FAD · Flavin-adenine dinucleotide · ligand · chains A
- GSH · Glutathione · ligand · chains A
- MG · Magnesium ion · metal · chains A
- EDO · 1,2-ethanediol · additive · 5 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 657 | 0.74 | 0.80 | 69 | FAD |
| 2 | 83 | 0.52 | 0.84 | 19 | EDO |
| 3 | 172 | 0.51 | 0.78 | 33 | GSH, MG, EDO |
| 4 | 164 | 0.44 | 0.75 | 19 | empty |
| 5 | 61 | 0.37 | 0.79 | 16 | empty |
Modifications
Observed in the structure: 14 modified, 1 covalent (engineered, covalent ligand).
Compared structures
- 3G5S · Crystal structure of Thermus thermophilus TrmFO in complex with glutathione · the same entry in another collection · chain A against A, TM-score 1.00
- Q5SID2 · AlphaFold monomer V2.0 prediction for methylenetetrahydrofolate… · a predicted model of the same protein · chain A against A, TM-score 0.70
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 Q5SID2
- Elsewhere: RCSB PDB 3G5S · PDBe 3G5S · UniProt Q5SID2
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