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An orthogonal seryl-tRNA SYNTHETASE/TRNA pair for noncanonical amino acid mutagenesis in escherichia COLI
Analyse An orthogonal seryl-tRNA SYNTHETASE/TRNA pair for noncanonical amino acid… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6X94
- Type
- protein
- Length
- 413 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Serine--tRNA ligase
- EC
- 6.1.1.11
- UniProt
- Q8PYJ6
- Ligands
- SSA, K, SCN, CL
- Pockets
- 3 · best druggability 0.73
Structure
x-ray diffraction · 1 distinct chain · 46% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Serine--tRNA ligase (EC 6.1.1.11) | protein | 413 | 46% helix, 20% strand | Q8PYJ6 |
Ligands and binding sites
- SSA · 5'-O-(N-(L-seryl)-sulfamoyl)adenosine · ligand · chains A
- K · Potassium ion · metal · chains A
- SCN · Thiocyanate ion · ion · 5 copies · chains A
- CL · Chloride ion · ion · chains A
- PEG · Di(hydroxyethyl)ether · additive · 3 copies · chains A
- DMS · Dimethyl sulfoxide · additive · 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 | 532 | 0.73 | 0.81 | 44 | SSA, SCN |
| 2 | 110 | 0.40 | 0.76 | 21 | SCN |
| 3 | 57 | 0.34 | 0.78 | 17 | empty |
Compared structures
- 6X94 · An orthogonal seryl-tRNA synthetase/tRNA pair for noncanonical amino acid mutagenesis in… · the same entry in another collection · chain A against A, TM-score 1.00
- Q8PYJ6 · AlphaFold monomer V2.0 prediction for serine--tRNA ligase (Q8PYJ6) · a predicted model of the same protein · chain A 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 Q8PYJ6
- Elsewhere: RCSB PDB 6X94 · PDBe 6X94 · UniProt Q8PYJ6
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