Research workbench
E. COLI cysteinyl-tRNA and T. aquaticus elongation factor ef-TU:GTP ternary complex
Analyse E. COLI cysteinyl-tRNA and T. aquaticus elongation factor ef-TU:GTP ternary… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1B23
- Type
- protein + RNA
- Length
- 479 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cysteinyl tRNA; Elongation factor tu
- UniProt
- Q01698
- Ligands
- CYS, GNP, MG, SO4
- Pockets
- 7 · best druggability 0.79
Structure
x-ray diffraction · 2 distinct chains · 24% helix, 34% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| R | Cysteinyl tRNA | rna | 74 | — | — |
| P | Elongation factor tu | protein | 405 | 24% helix, 34% strand | Q01698 |
Ligands and binding sites
- CYS · Cysteine · ligand · chains R, P
- GNP · Phosphoaminophosphonic acid-guanylate ester · ligand · chains P
- MG · Magnesium ion · metal · 3 copies · chains R, P
- SO4 · Sulfate ion · ion · 2 copies · chains R, P
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 738 | 0.79 | 0.83 | 66 | CYS |
| 2 | 389 | 0.54 | 0.74 | 24 | empty |
| 3 | 211 | 0.52 | 0.77 | 26 | empty |
| 4 | 72 | 0.45 | 0.82 | 23 | MG, GNP |
| 5 | 58 | 0.35 | 0.79 | 11 | empty |
Interfaces
1 interface between chains.
- R–P · 1354 Ų buried · 35 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 8 modified, 1 covalent (nucleotide modification, covalent ligand).
Compared structures
- 1B23 · E. coli cysteinyl-tRNA and T. aquaticus elongation factor EF-TU:GTP ternary complex · the same entry in another collection · chain R against R, TM-score 1.00
- Q01698 · AlphaFold monomer V2.0 prediction for elongation factor tu (Q01698) · a predicted model of the same protein · chain P against A, TM-score 0.99
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 Q01698
- Elsewhere: RCSB PDB 1B23 · PDBe 1B23 · UniProt Q01698
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