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Crystal structure of the catalytic domain of mmomers, an O-methyl tyrosyl-tRNA synthetase evolved from methanosarcina mazei pylrs, complexed with O-methyl tyrosine and AMP-pnp
Analyse Crystal structure of the catalytic domain of mmomers, an O-methyl tyrosyl-tRNA… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3QTC
- Type
- protein
- Length
- 257 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Pyrrolysyl-tRNA synthetase
- EC
- 6.1.1.26
- UniProt
- Q8PWY1
- Ligands
- 0A1, ANP, MG
- Pockets
- 3 · best druggability 0.69
Structure
x-ray diffraction · 1 distinct chain · 39% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Pyrrolysyl-tRNA synthetase (EC 6.1.1.26) | protein | 257 | 39% helix, 23% strand | Q8PWY1 |
Ligands and binding sites
- 0A1 · O-methyl-L-tyrosine · ligand · chains A
- ANP · Phosphoaminophosphonic acid-adenylate ester · ligand · chains A
- MG · Magnesium ion · metal · 2 copies · chains A
- EDO · 1,2-ethanediol · additive · 5 copies · chains A
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 | 402 | 0.69 | 0.81 | 40 | MG, 0A1, EDO, ANP |
| 2 | 80 | 0.35 | 0.76 | 18 | empty |
| 3 | 61 | 0.32 | 0.76 | 12 | empty |
Compared structures
- 3QTC · Crystal structure of the catalytic domain of MmOmeRS, an O-methyl tyrosyl-tRNA synthetase… · the same entry in another collection · chain A against A, TM-score 1.00
- Q8PWY1 · AlphaFold monomer V2.0 prediction for pyrrolysine--tRNA ligase (Q8PWY1) · a predicted model of the same protein · chain A against A, TM-score 0.99
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 Q8PWY1
- Elsewhere: RCSB PDB 3QTC · PDBe 3QTC · UniProt Q8PWY1
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