Research workbench
Crystal structure of dual specific TRM10 construct from thermococcus kodakaraensis.
Analyse Crystal structure of dual specific TRM10 construct from thermococcus… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6EMT
- Type
- protein
- Length
- 167 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- TRNA (GUANINE(9)-/ADENINE(9)-N1)-methyltransferase
- EC
- 2.1.1.218, 2.1.1.221
- UniProt
- Q5JD38
- Pockets
- 1 · best druggability 0.58
Structure
x-ray diffraction · 1 distinct chain · 38% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | TRNA (GUANINE(9)-/ADENINE(9)-N1)-methyltransferase (EC 2.1.1.218, 2.1.1.221) | protein | 167 | 38% helix, 19% strand | Q5JD38 |
Ligands and binding sites
- ACT · Acetate ion · additive · 8 copies · chains A
- GOL · Glycerol · additive · 2 copies · chains A
- TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 263 | 0.58 | 0.78 | 32 | empty |
Compared structures
- 6EMT · Crystal Structure of dual specific Trm10 construct from Thermococcus kodakaraensis. · the same entry in another collection · chain A against A, TM-score 1.00
- Q5JD38 · AlphaFold monomer V2.0 prediction for tRNA (GUANINE(9)-/ADENINE(9)-N1)-methyltransferase… · a predicted model of the same protein · chain A against A, TM-score 0.97
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 Q5JD38
- Elsewhere: RCSB PDB 6EMT · PDBe 6EMT · UniProt Q5JD38
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