Research workbench
Mutant T252A of E. COLI leucyl-tRNA synthetase, TRNA(LEU) and leucyl- adenylate analogue in the aminoacylation conformation
Analyse Mutant T252A of E. COLI leucyl-tRNA synthetase, TRNA(LEU) and leucyl- adenylate… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5OMW
- Type
- protein + RNA
- Length
- 1,879 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Leucine--tRNA ligase; L-leucyl-tRNA
- EC
- 6.1.1.4
- UniProt
- P07813
- Ligands
- LSS, ZN, MG
- Pockets
- 20 · best druggability 0.82
Structure
x-ray diffraction · 3 distinct chains · 39% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | Leucine--tRNA ligase (EC 6.1.1.4) | protein | 860 | 39% helix, 22% strand | P07813 |
| B | L-leucyl-tRNA | rna | 83 | — | — |
| E | L-leucyl-tRNA | rna | 76 | — | — |
Ligands and binding sites
- LSS · 5'-O-(L-leucylsulfamoyl)adenosine · ligand · 2 copies · chains A, B, D, E
- ZN · Zinc ion · metal · 2 copies · chains A, D
- MG · Magnesium ion · metal · 2 copies · chains B, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 221 | 0.82 | 0.95 | 30 | LSS |
| 2 | 1072 | 0.82 | 0.83 | 87 | LSS |
| 3 | 1147 | 0.78 | 0.80 | 82 | empty |
| 4 | 910 | 0.74 | 0.78 | 66 | empty |
| 5 | 905 | 0.74 | 0.79 | 56 | empty |
Interfaces
4 interfaces between chains.
- D–E · 3031 Ų buried · 47 hydrogen bonds · protein-nucleic
- A–B · 2993 Ų buried · 54 hydrogen bonds · protein-nucleic
- A–D · 646 Ų buried · 6 hydrogen bonds · protein-protein
- B–D · 96 Ų buried · 2 hydrogen bonds · protein-nucleic
Compared structures
- 5OMW · Mutant T252A of E. coli leucyl-tRNA synthetase, tRNA(leu) and leucyl-adenylate analogue… · the same entry in another collection · chain A against A, TM-score 1.00
- P07813 · AlphaFold monomer V2.0 prediction for leucine--tRNA ligase (P07813) · a predicted model of the same protein · chain A against A, TM-score 0.88
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 P07813
- Elsewhere: RCSB PDB 5OMW · PDBe 5OMW · UniProt P07813
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