MolNFT v1 · #121049 · protein
Crystal structure of pyrococcus abyssi TRM5A complexed with mta
5HJM · TRNA (GUANINE(37)-N1)-methyltransferase TRM5A: “Crystal structure of pyrococcus abyssi TRM5A complexed with mta”. X-ray diffraction, 2 ligands (MTA, HSL), 3 pockets (best druggability 0.78). MolNFT v1 #121049 on GenesisL1: 3D…
- PDB
- 5HJM
- Type
- protein
- Length
- 349 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- TRNA (GUANINE(37)-N1)-methyltransferase TRM5A
- EC
- 2.1.1.228
- UniProt
- Q9V2G1
- Ligands
- MTA, HSL
- Pockets
- 3 · best druggability 0.78
Structure
x-ray diffraction · 1 distinct chain · 34% helix, 34% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | TRNA (GUANINE(37)-N1)-methyltransferase TRM5A (EC 2.1.1.228) | protein | 349 | 34% helix, 34% strand | Q9V2G1 |
Ligands and binding sites
- MTA · 5'-deoxy-5'-methylthioadenosine · ligand · chains A
- HSL · Homoserine lactone · ligand · chains A
- ACT · Acetate ion · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 435 | 0.78 | 0.86 | 53 | MTA, ACT |
| 2 | 235 | 0.46 | 0.73 | 24 | empty |
| 3 | 87 | 0.38 | 0.76 | 17 | HSL |
Compared structures
- 5HJM · Crystal Structure of Pyrococcus abyssi Trm5a complexed with MTA · the same entry in another collection · chain A against A, TM-score 1.00
- Q9V2G1 · AlphaFold monomer V2.0 prediction for tRNA (GUANINE(37)-N1)/4-DEMETHYLWYOSINE(37)-methyltr… · a predicted model of the same protein · chain A against A, TM-score 0.77
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 Q9V2G1
- Elsewhere: RCSB PDB 5HJM · PDBe 5HJM · UniProt Q9V2G1
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