Research workbench
Crystal structure of full length E.COLI trmj in complex with sah
Analyse Crystal structure of full length E.COLI trmj in complex with sah in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4XBO
- Type
- protein
- Length
- 454 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
- 5 · best druggability 0.80
Structure
x-ray diffraction · 2 distinct chains · 46% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | TRNA (CYTIDINE/URIDINE-2'-O-)-methyltransferase trmj (EC 2.1.1.200) | protein | 228 | 45% helix, 13% strand | P0AE01 |
| B | TRNA (CYTIDINE/URIDINE-2'-O-)-methyltransferase trmj (EC 2.1.1.200) | protein | 226 | 48% helix, 13% strand | P0AE01 |
Ligands and binding sites
- SAH · S-adenosyl-L-homocysteine · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 110 | 0.80 | 0.98 | 22 | empty |
| 2 | 209 | 0.65 | 0.84 | 26 | SAH |
| 3 | 197 | 0.61 | 0.82 | 26 | SAH |
| 4 | 83 | 0.53 | 0.85 | 15 | empty |
| 5 | 86 | 0.36 | 0.76 | 24 | empty |
Interfaces
1 interface between chains.
- A–B · 2316 Ų buried · 35 hydrogen bonds · protein-protein
Compared structures
- 4XBO · Crystal structure of full length E.coli TrmJ in complex with SAH · 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 0.97
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 4XBO · PDBe 4XBO · UniProt P0AE01
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