Research workbench
T. aquaticus elongation factor ef-tu complexed with the antibiotic enacyloxin iia, a GTP analog, and phe-tRNA
Analyse T. aquaticus elongation factor ef-tu complexed with the antibiotic enacyloxin… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1OB5
- Type
- protein + RNA
- Length
- 1,428 residues
- Chains
- 6
- 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
- Q01698
- Ligands
- PHA, GNP, ENX, MG
- Pockets
- 20 · best druggability 0.80
Structure
x-ray diffraction · 2 distinct chains · 21% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, E | Elongation factor tu (EC 3.6.1.48) | protein | 400 | 21% helix, 23% strand | Q01698 |
| B, D, F | Transfer-RNA, phe | rna | 76 | — | — |
Ligands and binding sites
- PHA · Phenylalaninal · ligand · 3 copies · chains A, B, C, D, E, F
- GNP · Phosphoaminophosphonic acid-guanylate ester · ligand · 3 copies · chains A, C, E
- ENX · Enacyloxin iia · ligand · 3 copies · chains A, C, E
- MG · Magnesium ion · metal · 3 copies · chains A, C, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 15 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 952 | 0.80 | 0.82 | 80 | PHA |
| 2 | 976 | 0.80 | 0.82 | 82 | PHA |
| 3 | 474 | 0.79 | 0.87 | 55 | PHA |
| 4 | 531 | 0.72 | 0.81 | 67 | empty |
| 5 | 380 | 0.71 | 0.84 | 30 | empty |
Interfaces
9 interfaces between chains.
- E–F · 1364 Ų buried · 48 hydrogen bonds · protein-nucleic
- C–D · 1362 Ų buried · 48 hydrogen bonds · protein-nucleic
- A–B · 1360 Ų buried · 48 hydrogen bonds · protein-nucleic
- D–F · 349 Ų buried · 14 hydrogen bonds · nucleic-nucleic
- B–F · 348 Ų buried · 14 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 42 modified, 3 covalent (nucleotide modification, covalent ligand).
Compared structures
- 1OB5 · T. aquaticus elongation factor EF-Tu complexed with the antibiotic enacyloxin IIa, a GTP… · the same entry in another collection · chain F against F, TM-score 1.00
- Q01698 · AlphaFold monomer V2.0 prediction for elongation factor tu (Q01698) · a predicted model of the same protein · chain E against A, TM-score 0.92
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 1OB5 · PDBe 1OB5 · UniProt Q01698
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