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Crystal structure of mycoplasma mobile leucyl-tRNA synthetase with leu-ams in the active site
Analyse Crystal structure of mycoplasma mobile leucyl-tRNA synthetase with leu-ams in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3ZIU
- Type
- protein
- Length
- 1,196 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Leucyl-tRNA synthetase
- EC
- 6.1.1.4
- UniProt
- Q6KHA5
- Ligands
- LSS
- Pockets
- 13 · best druggability 0.86
Structure
x-ray diffraction · 2 distinct chains · 43% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Leucyl-tRNA synthetase (EC 6.1.1.4) | protein | 621 | 42% helix, 17% strand | Q6KHA5 |
| B | Leucyl-tRNA synthetase (EC 6.1.1.4) | protein | 575 | 45% helix, 15% strand | Q6KHA5 |
Ligands and binding sites
- LSS · 5'-O-(L-leucylsulfamoyl)adenosine · ligand · 2 copies · chains A, B
- GOL · Glycerol · additive · 10 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1070 | 0.86 | 0.88 | 113 | GOL |
| 2 | 546 | 0.78 | 0.84 | 66 | LSS, GOL |
| 3 | 485 | 0.73 | 0.82 | 54 | LSS |
| 4 | 112 | 0.55 | 0.83 | 22 | empty |
| 5 | 112 | 0.49 | 0.80 | 22 | empty |
Interfaces
1 interface between chains.
- A–B · 786 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 3ZIU · Crystal structure of Mycoplasma mobile Leucyl-tRNA Synthetase with Leu-AMS in the active… · the same entry in another collection · 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 Q6KHA5
- Elsewhere: RCSB PDB 3ZIU · PDBe 3ZIU · UniProt Q6KHA5
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