Research workbench
E. COLI elongation factor ef-tu complexed with the antibiotic kirromycin, a GTP analog, and phe-tRNA
Analyse E. COLI elongation factor ef-tu complexed with the antibiotic kirromycin, a GTP… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1OB2
- Type
- protein + RNA
- Length
- 469 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Elongation factor tu; Transfer-RNA, phe
- EC
- 3.6.1.48
- UniProt
- P0CE48
- Ligands
- PHA, KIR, GNP, GLC, FRU, MG
- Pockets
- 8 · best druggability 0.78
Structure
x-ray diffraction · 2 distinct chains · 25% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Elongation factor tu (EC 3.6.1.48) | protein | 393 | 25% helix, 30% strand | P0CE48 |
| B | Transfer-RNA, phe | rna | 76 | — | — |
Ligands and binding sites
- PHA · Phenylalaninal · ligand · chains A, B
- KIR · Kirromycin · ligand · chains A
- GNP · Phosphoaminophosphonic acid-guanylate ester · ligand · chains A
- GLC · alpha-D-glucopyranose · sugar · chains A
- FRU · beta-D-fructofuranose · sugar · chains A
- MG · Magnesium ion · metal · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 907 | 0.78 | 0.81 | 86 | PHA |
| 2 | 424 | 0.65 | 0.78 | 55 | KIR |
| 3 | 278 | 0.56 | 0.78 | 21 | empty |
| 4 | 298 | 0.51 | 0.75 | 22 | empty |
| 5 | 67 | 0.44 | 0.83 | 13 | empty |
Interfaces
1 interface between chains.
- A–B · 1278 Ų buried · 30 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 13 modified, 1 covalent (nucleotide modification, covalent ligand).
Compared structures
- 1OB2 · E. coli elongation factor EF-Tu complexed with the antibiotic kirromycin, a GTP analog… · the same entry in another collection · chain A against A, TM-score 1.00
- P0CE48 · AlphaFold monomer V2.0 prediction for elongation factor tu 2 (P0CE48) · a predicted model of the same protein · chain A against A, TM-score 0.93
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 P0CE48
- Elsewhere: RCSB PDB 1OB2 · PDBe 1OB2 · UniProt P0CE48
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