MolNFT v1 · #120004 · protein
Methylation at position 32 of tRNA catalyzed by trmj alters oxidative stress response in pseudomonas aeruiginosa
5GM8 · TRNA (CYTIDINE/URIDINE-2'-O-)-methyltransferase trmj: “Methylation at position 32 of tRNA catalyzed by trmj alters oxidative stress response in pseudomonas…”. X-ray diffraction, 1 ligand (SFG), 4 pockets (best druggability 0.79).…
- 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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