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
- 6EMU
- Type
- protein
- Length
- 507 residues
- Chains
- 3
- 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
- Ligands
- SAM
- Pockets
- 4 · best druggability 0.76
Structure
x-ray diffraction · 3 distinct chains · 42% helix, 18% 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 | 170 | 42% helix, 18% strand | Q5JD38 |
| B | TRNA (GUANINE(9)-/ADENINE(9)-N1)-methyltransferase (EC 2.1.1.218, 2.1.1.221) | protein | 168 | 42% helix, 19% strand | Q5JD38 |
| C | TRNA (GUANINE(9)-/ADENINE(9)-N1)-methyltransferase (EC 2.1.1.218, 2.1.1.221) | protein | 169 | 42% helix, 18% strand | Q5JD38 |
Ligands and binding sites
- SAM · S-adenosylmethionine · ligand · 3 copies · chains A, B, C
- GOL · Glycerol · additive · 2 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 857 | 0.76 | 0.79 | 73 | SAM |
| 2 | 179 | 0.63 | 0.84 | 25 | SAM |
| 3 | 166 | 0.60 | 0.83 | 22 | SAM |
| 4 | 131 | 0.50 | 0.79 | 26 | GOL |
Interfaces
3 interfaces between chains.
- B–C · 455 Ų buried · 5 hydrogen bonds · protein-protein
- A–B · 333 Ų buried · 5 hydrogen bonds · protein-protein
- A–C · 250 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 6EMU · Crystal Structure of dual specific Trm10 construct from Thermococcus kodakaraensis. · the same entry in another collection · chain C against C, 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 B against A, TM-score 0.98
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 6EMU · PDBe 6EMU · UniProt Q5JD38
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