Research workbench
Crystal structure of tRNA (UM34/CM34) methyltransferase trml from escherichia COLI with sah
Analyse Crystal structure of tRNA (UM34/CM34) methyltransferase trml from escherichia… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4JAL
- Type
- protein
- Length
- 311 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- TRNA (CYTIDINE(34)-2'-O)-methyltransferase
- EC
- 2.1.1.207
- UniProt
- P0AGJ7
- Ligands
- SAH
- Pockets
- 1 · best druggability 0.75
Structure
x-ray diffraction · 2 distinct chains · 36% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | TRNA (CYTIDINE(34)-2'-O)-methyltransferase (EC 2.1.1.207) | protein | 156 | 36% helix, 18% strand | P0AGJ7 |
| B | TRNA (CYTIDINE(34)-2'-O)-methyltransferase (EC 2.1.1.207) | protein | 155 | 36% helix, 18% strand | P0AGJ7 |
Ligands and binding sites
- SAH · S-adenosyl-L-homocysteine · ligand · 2 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 2 copies · chains A, B
- EPE · 4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 635 | 0.75 | 0.81 | 83 | SAH, EPE, EDO |
Interfaces
1 interface between chains.
- A–B · 1389 Ų buried · 32 hydrogen bonds · protein-protein
Compared structures
- 4JAL · Crystal structure of tRNA (Um34/Cm34) methyltransferase TrmL from Escherichia coli with… · the same entry in another collection · chain A against A, TM-score 1.00
- P0AGJ7 · AlphaFold monomer V2.0 prediction for tRNA (CYTIDINE(34)-2'-O)-methyltransferase (P0AGJ7) · a predicted model of the same protein · chain A 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 P0AGJ7
- Elsewhere: RCSB PDB 4JAL · PDBe 4JAL · UniProt P0AGJ7
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