MolNFT v1 · #182620 · protein
Crystal structure of a tRNA (guanine-N1)-methyltransferase from acinetobacter baumannii AB5075-uw bound to S-adenosyl homocysteine
7MYS · TRNA (guanine-N(1)-)-methyltransferase: “Crystal structure of a tRNA (guanine-N1)-methyltransferase from acinetobacter baumannii AB5075-uw bound to…”. X-ray diffraction, 1 ligand (SAH), 3 pockets (best druggability 0.79). MolNFT v1…
- PDB
- 7MYS
- Type
- protein
- Length
- 478 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- TRNA (guanine-N(1)-)-methyltransferase
- EC
- 2.1.1.228
- UniProt
- A0A0D5YDX5
- Ligands
- SAH
- Pockets
- 3 · best druggability 0.79
Structure
x-ray diffraction · 2 distinct chains · 42% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | TRNA (guanine-N(1)-)-methyltransferase (EC 2.1.1.228) | protein | 239 | 43% helix, 17% strand | A0A0D5YDX5 |
| B | TRNA (guanine-N(1)-)-methyltransferase (EC 2.1.1.228) | protein | 239 | 41% helix, 18% strand | A0A0D5YDX5 |
Ligands and binding sites
- SAH · S-adenosyl-L-homocysteine · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 196 | 0.79 | 0.94 | 34 | SAH |
| 2 | 412 | 0.76 | 0.86 | 58 | SAH |
| 3 | 180 | 0.56 | 0.80 | 26 | empty |
Interfaces
1 interface between chains.
- A–B · 3687 Ų buried · 61 hydrogen bonds · protein-protein
Compared structures
- 7MYS · Crystal structure of a tRNA (guanine-N1)-methyltransferase from Acinetobacter baumannii… · the same entry in another collection · chain B against B, 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 A0A0D5YDX5
- Elsewhere: RCSB PDB 7MYS · PDBe 7MYS · UniProt A0A0D5YDX5
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