MolNFT v1 · #55746 · protein
Complex structure of TRM1 from pyrococcus horikoshii with S- adenosyl-L-homocystein in the orthorhombic crystal-lattice
2YTZ · N(2),N(2)-dimethylguanosine tRNA methyltransferase: “Complex structure of TRM1 from pyrococcus horikoshii with S- adenosyl-L-homocystein in the orthorhombic…”. X-ray diffraction, 2 ligands (SAH, SO4), 6 pockets (best druggability…
- PDB
- 2YTZ
- Type
- protein
- Length
- 736 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- N(2),N(2)-dimethylguanosine tRNA methyltransferase
- EC
- 2.1.1.32
- UniProt
- O59493
- Ligands
- SAH, SO4
- Pockets
- 6 · best druggability 0.60
Structure
x-ray diffraction · 2 distinct chains · 39% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | N(2),N(2)-dimethylguanosine tRNA methyltransferase (EC 2.1.1.32) | protein | 371 | 40% helix, 28% strand | O59493 |
| B | N(2),N(2)-dimethylguanosine tRNA methyltransferase (EC 2.1.1.32) | protein | 365 | 39% helix, 27% strand | O59493 |
Ligands and binding sites
- SAH · S-adenosyl-L-homocysteine · ligand · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 195 | 0.60 | 0.81 | 35 | SAH |
| 2 | 191 | 0.59 | 0.81 | 33 | SAH |
| 3 | 143 | 0.40 | 0.74 | 24 | empty |
| 4 | 103 | 0.35 | 0.73 | 19 | empty |
| 5 | 65 | 0.30 | 0.74 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 1651 Ų buried · 13 hydrogen bonds · protein-protein
Compared structures
- 2YTZ · Complex structure of Trm1 from Pyrococcus horikoshii with S-adenosyl-L-Homocystein in the… · the same entry in another collection · chain B against B, TM-score 1.00
- O59493 · AlphaFold monomer V2.0 prediction for tRNA (GUANINE(26)-N(2))-dimethyltransferase (O59493) · a predicted model of the same protein · chain B 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 O59493
- Elsewhere: RCSB PDB 2YTZ · PDBe 2YTZ · UniProt O59493
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