Research workbench
Methylation at position 32 of tRNA catalyzed by trmj alters oxidative stress response in pseudomonas aeruiginosa
Analyse Methylation at position 32 of tRNA catalyzed by trmj alters oxidative stress… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5GM8
- Type
- protein
- Length
- 684 residues
- Chains
- 4
- 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
- A0A072ZPM2
- Ligands
- SFG
- Pockets
- 4 · best druggability 0.79
Structure
x-ray diffraction · 3 distinct chains · 42% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | TRNA (CYTIDINE/URIDINE-2'-O-)-methyltransferase trmj (EC 2.1.1.200) | protein | 170 | 40% helix, 18% strand | A0A072ZPM2 |
| B | TRNA (CYTIDINE/URIDINE-2'-O-)-methyltransferase trmj (EC 2.1.1.200) | protein | 173 | 43% helix, 17% strand | A0A072ZPM2 |
| D | TRNA (CYTIDINE/URIDINE-2'-O-)-methyltransferase trmj (EC 2.1.1.200) | protein | 171 | 44% helix, 19% strand | A0A072ZPM2 |
Ligands and binding sites
- SFG · Sinefungin · ligand · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 676 | 0.79 | 0.84 | 90 | SFG |
| 2 | 94 | 0.71 | 0.94 | 22 | empty |
| 3 | 548 | 0.68 | 0.78 | 63 | SFG |
| 4 | 302 | 0.67 | 0.82 | 50 | SFG |
Interfaces
3 interfaces between chains.
- A–B · 1242 Ų buried · 18 hydrogen bonds · protein-protein
- C–D · 1237 Ų buried · 18 hydrogen bonds · protein-protein
- B–C · 264 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 5GM8 · Methylation at position 32 of tRNA catalyzed by TrmJ alters oxidative stress response in… · the same entry in another collection · chain B against B, TM-score 1.00
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 A0A072ZPM2
- Elsewhere: RCSB PDB 5GM8 · PDBe 5GM8 · UniProt A0A072ZPM2
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