MolNFT v1 · #120008 · protein
Methylation at position 32 of tRNA catalyzed by trmj alters oxidative stress response in pseudomonas aeruiginosa
5GMC · 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, 5 pockets (best druggability 0.80). MolNFT v1 #120008…
- PDB
- 5GMC
- Type
- protein
- Length
- 686 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
- Pockets
- 5 · best druggability 0.80
Structure
x-ray diffraction · 4 distinct chains · 43% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | TRNA (CYTIDINE/URIDINE-2'-O-)-methyltransferase trmj (EC 2.1.1.200) | protein | 174 | 44% helix, 19% strand | A0A072ZPM2 |
| B | TRNA (CYTIDINE/URIDINE-2'-O-)-methyltransferase trmj (EC 2.1.1.200) | protein | 171 | 43% helix, 18% strand | A0A072ZPM2 |
| C | TRNA (CYTIDINE/URIDINE-2'-O-)-methyltransferase trmj (EC 2.1.1.200) | protein | 169 | 43% helix, 18% strand | A0A072ZPM2 |
| D | TRNA (CYTIDINE/URIDINE-2'-O-)-methyltransferase trmj (EC 2.1.1.200) | protein | 172 | 42% helix, 18% strand | A0A072ZPM2 |
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1198 | 0.80 | 0.81 | 128 | empty |
| 2 | 97 | 0.63 | 0.89 | 25 | empty |
| 3 | 130 | 0.63 | 0.87 | 24 | empty |
| 4 | 72 | 0.47 | 0.83 | 16 | empty |
| 5 | 55 | 0.26 | 0.72 | 13 | empty |
Interfaces
5 interfaces between chains.
- A–B · 1285 Ų buried · 21 hydrogen bonds · protein-protein
- C–D · 1222 Ų buried · 10 hydrogen bonds · protein-protein
- A–D · 124 Ų buried · 2 hydrogen bonds · protein-protein
- B–C · 123 Ų buried · 3 hydrogen bonds · protein-protein
- B–D · 91 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 5GMC · Methylation at position 32 of tRNA catalyzed by TrmJ alters oxidative stress response in… · the same entry in another collection · chain A against A, 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 5GMC · PDBe 5GMC · UniProt A0A072ZPM2
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