MolNFT v1 · #115512 · protein
Structure of Y. lipolytica TRM9-TRM112 complex, a methyltransferase modifying U34 in the anticodon loop of some trnas
5CM2 · TRNA methyltransferase: “Structure of Y. lipolytica TRM9-TRM112 complex, a methyltransferase modifying U34 in the anticodon loop of…”. X-ray diffraction, 1 ligand (ZN), 3 pockets (best druggability 0.60). MolNFT v1 #115512 on…
- PDB
- 5CM2
- Type
- protein
- Length
- 308 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- TRNA methyltransferase; TRNA methyltransferase activator subunit
- UniProt
- Q6C999, Q6C4P5
- Ligands
- ZN
- Pockets
- 3 · best druggability 0.60
Structure
x-ray diffraction · 2 distinct chains · 27% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| Z | TRNA methyltransferase | protein | 184 | 22% helix, 40% strand | Q6C999 |
| M | TRNA methyltransferase activator subunit | protein | 124 | 35% helix, 22% strand | Q6C4P5 |
Ligands and binding sites
- ZN · Zinc ion · metal · chains M
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 | 237 | 0.60 | 0.80 | 25 | empty |
| 2 | 204 | 0.46 | 0.74 | 26 | empty |
| 3 | 74 | 0.39 | 0.78 | 16 | empty |
Interfaces
1 interface between chains.
- Z–M · 1192 Ų buried · 20 hydrogen bonds · protein-protein
Compared structures
- 5CM2 · Structure of Y. lipolytica Trm9-Trm112 complex, a methyltransferase modifying U34 in the… · the same entry in another collection · chain Z against Z, 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 Q6C999
- Every structure of UniProt Q6C4P5
- Elsewhere: RCSB PDB 5CM2 · PDBe 5CM2 · UniProt Q6C999 · UniProt Q6C4P5
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