MolNFT v1 · #32721 · protein + RNA
Thermus thermophilus leucyl-tRNA synthetase complexed with a trnaleu transcript in the post-editing conformation
2BYT: “Thermus thermophilus leucyl-tRNA synthetase complexed with a trnaleu transcript in the post-editing…”. X-ray diffraction, 4 ligands (LEU, ZN, HG), 20 pockets (best druggability 0.78). MolNFT v1 #32721 on GenesisL1: 3D structure…
- PDB
- 2BYT
- Type
- protein + RNA
- Length
- 1,908 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Leucyl-tRNA synthetase; Trnaleu transcript with anticodon cag
- UniProt
- Q7SIE4
- Ligands
- LEU, ZN, HG, SO4
- Pockets
- 20 · best druggability 0.78
Structure
x-ray diffraction · 2 distinct chains · 37% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | Leucyl-tRNA synthetase | protein | 876 | 37% helix, 19% strand | Q7SIE4 |
| B, E | Trnaleu transcript with anticodon cag | rna | 78 | — | — |
Ligands and binding sites
- 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 · 15 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, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 757 | 0.78 | 0.83 | 84 | LEU, SO4 |
| 2 | 725 | 0.77 | 0.82 | 84 | LEU, SO4 |
| 3 | 605 | 0.75 | 0.81 | 56 | SO4 |
| 4 | 576 | 0.74 | 0.82 | 55 | SO4 |
| 5 | 516 | 0.71 | 0.81 | 34 | empty |
Interfaces
5 interfaces between chains.
- D–E · 2147 Ų buried · 25 hydrogen bonds · protein-nucleic
- A–B · 2131 Ų buried · 29 hydrogen bonds · protein-nucleic
- B–E · 627 Ų buried · 30 hydrogen bonds · nucleic-nucleic
- A–E · 27 Ų buried · 0 hydrogen bonds · protein-nucleic
- B–D · 23 Ų buried · 0 hydrogen bonds · protein-nucleic
Compared structures
- 2BYT · Thermus thermophilus Leucyl-tRNA synthetase complexed with a tRNAleu transcript in the… · the same entry in another collection · chain B against B, 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 2BYT · PDBe 2BYT · UniProt Q7SIE4
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