MolNFT v1 · #121047 · protein
Crystal structure of pyrococcus abyssi TRM5A complexed with sah
5HJK · TRNA (GUANINE(37)-N1)-methyltransferase TRM5A: “Crystal structure of pyrococcus abyssi TRM5A complexed with sah”. X-ray diffraction, 1 ligand (SAH), 3 pockets (best druggability 0.77). MolNFT v1 #121047 on GenesisL1: 3D structure…
- PDB
- 5HJK
- Type
- protein
- Length
- 347 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
- SAH
- Pockets
- 3 · best druggability 0.77
Structure
x-ray diffraction · 1 distinct chain · 33% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | TRNA (GUANINE(37)-N1)-methyltransferase TRM5A (EC 2.1.1.228) | protein | 347 | 33% helix, 32% strand | Q9V2G1 |
Ligands and binding sites
- SAH · S-adenosyl-L-homocysteine · ligand · 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 | 458 | 0.77 | 0.85 | 53 | SAH |
| 2 | 243 | 0.45 | 0.72 | 28 | empty |
| 3 | 82 | 0.37 | 0.76 | 17 | empty |
Compared structures
- 5HJK · Crystal Structure of Pyrococcus abyssi Trm5a complexed with SAH · 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 0.76
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 5HJK · PDBe 5HJK · UniProt Q9V2G1
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