MolNFT v1 · #88192 · protein
Crystal structure of E.COLI trmj in complex with S-adenosyl-L- homocysteine
4CNE · TRNA (CYTIDINE/URIDINE-2'-O-)-methyltransferase trmj: “Crystal structure of E.COLI trmj in complex with S-adenosyl-L- homocysteine”. X-ray diffraction, 1 ligand (SAH), 3 pockets (best druggability 0.60). MolNFT v1 #88192 on…
- PDB
- 4CNE
- Type
- protein
- Length
- 333 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- TRNA (CYTIDINE/URIDINE-2'-O-)-methyltransferase trmj
- EC
- 2.1.1.200
- UniProt
- P0AE01
- Ligands
- SAH
- Pockets
- 3 · best druggability 0.60
Structure
x-ray diffraction · 2 distinct chains · 43% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | TRNA (CYTIDINE/URIDINE-2'-O-)-methyltransferase trmj (EC 2.1.1.200) | protein | 169 | 42% helix, 18% strand | P0AE01 |
| B | TRNA (CYTIDINE/URIDINE-2'-O-)-methyltransferase trmj (EC 2.1.1.200) | protein | 164 | 45% helix, 19% strand | P0AE01 |
Ligands and binding sites
- SAH · S-adenosyl-L-homocysteine · ligand · 2 copies · chains A, B
- PEG · Di(hydroxyethyl)ether · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 133 | 0.60 | 0.85 | 20 | SAH |
| 2 | 211 | 0.57 | 0.79 | 25 | SAH |
| 3 | 190 | 0.51 | 0.77 | 31 | empty |
Interfaces
1 interface between chains.
- A–B · 1449 Ų buried · 24 hydrogen bonds · protein-protein
Compared structures
- 4CNE · Crystal structure of E.coli TrmJ in complex with S-adenosyl-L- homocysteine · the same entry in another collection · chain A against A, TM-score 1.00
- P0AE01 · AlphaFold monomer V2.0 prediction for tRNA (CYTIDINE/URIDINE-2'-O-)-methyltransferase… · a predicted model of the same protein · chain B against A, TM-score 0.96
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 P0AE01
- Elsewhere: RCSB PDB 4CNE · PDBe 4CNE · UniProt P0AE01
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