Research workbench
Structure of a mutant methionyl-tRNA synthetase with modified specificity complexed with azidonorleucine
Analyse Structure of a mutant methionyl-tRNA synthetase with modified specificity… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3H9B
- Type
- protein
- Length
- 544 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Methionyl-tRNA synthetase
- EC
- 6.1.1.10
- UniProt
- P00959
- Ligands
- NOT, ZN
- Pockets
- 2 · best druggability 0.64
Structure
x-ray diffraction · 1 distinct chain · 51% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Methionyl-tRNA synthetase (EC 6.1.1.10) | protein | 544 | 51% helix, 17% strand | P00959 |
Ligands and binding sites
- NOT · 6-azido-L-norleucine · ligand · chains A
- ZN · Zinc ion · metal · chains A
- CIT · Citric acid · additive · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 328 | 0.64 | 0.79 | 35 | NOT |
| 2 | 189 | 0.52 | 0.77 | 34 | CIT |
Compared structures
- 3H9B · Structure of a mutant methionyl-tRNA synthetase with modified specificity complexed with… · the same entry in another collection · chain A against A, TM-score 1.00
- P00959 · AlphaFold monomer V2.0 prediction for methionine--tRNA ligase (P00959) · 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 P00959
- Elsewhere: RCSB PDB 3H9B · PDBe 3H9B · UniProt P00959
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