Research workbench
Thermus thermophilus leucyl-tRNA synthetase complexed with with a trnaleu transcript in the post-editing conformation and a post-transfer editing substrate analogue
Analyse Thermus thermophilus leucyl-tRNA synthetase complexed with with a trnaleu… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2BTE
- Type
- protein + RNA
- Length
- 1,908 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Aminoacyl-tRNA synthetase; Trnaleu transcript with anticodon cag
- EC
- 6.1.1.4
- UniProt
- Q7SIE4
- Ligands
- NVA, 2AD, LEU, ZN, HG, SO4
- Pockets
- 20 · best druggability 0.80
Structure
x-ray diffraction · 2 distinct chains · 40% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | Aminoacyl-tRNA synthetase (EC 6.1.1.4) | protein | 876 | 40% helix, 20% strand | Q7SIE4 |
| B, E | Trnaleu transcript with anticodon cag | rna | 78 | — | — |
Ligands and binding sites
- NVA · Norvaline · ligand · 2 copies · chains A, D
- 2AD · 2'-amino-2'-deoxyadenosine · ligand · 2 copies · chains A, B, D, E
- LEU · Leucine · ligand · 2 copies · chains A, D
- ZN · Zinc ion · metal · 4 copies · chains A, D
- HG · Mercury (II) ion · metal · 2 copies · chains A, D
- SO4 · Sulfate ion · ion · 25 copies · chains A, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 13 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 982 | 0.80 | 0.82 | 89 | SO4, NVA, 2AD |
| 2 | 275 | 0.73 | 0.87 | 30 | NVA, 2AD |
| 3 | 578 | 0.72 | 0.80 | 60 | SO4, LEU |
| 4 | 297 | 0.72 | 0.85 | 39 | SO4, LEU |
| 5 | 480 | 0.72 | 0.82 | 32 | empty |
Interfaces
5 interfaces between chains.
- D–E · 1860 Ų buried · 27 hydrogen bonds · protein-nucleic
- A–B · 1768 Ų buried · 27 hydrogen bonds · protein-nucleic
- B–E · 628 Ų buried · 30 hydrogen bonds · nucleic-nucleic
- B–D · 114 Ų buried · 1 hydrogen bond · protein-nucleic
- A–E · 14 Ų buried · 0 hydrogen bonds · protein-nucleic
Compared structures
- 2BTE · Thermus thermophilus Leucyl-tRNA synthetase complexed with a tRNAleu transcript in the… · the same entry in another collection · chain D against D, 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 Q7SIE4
- Elsewhere: RCSB PDB 2BTE · PDBe 2BTE · UniProt Q7SIE4
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