Research workbench
Crystal structure of pseudomonas putida elongation factor tu (ef-tu)
Analyse Crystal structure of pseudomonas putida elongation factor tu (ef-tu) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4J0Q
- Type
- protein
- Length
- 1,861 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Elongation factor tu-a
- UniProt
- Q88QP8
- Ligands
- GDP, MG
- Pockets
- 15 · best druggability 0.71
Structure
x-ray diffraction · 4 distinct chains · 23% helix, 37% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Elongation factor tu-a | protein | 373 | 23% helix, 37% strand | Q88QP8 |
| B | Elongation factor tu-a | protein | 374 | 24% helix, 38% strand | Q88QP8 |
| D | Elongation factor tu-a | protein | 371 | 23% helix, 36% strand | Q88QP8 |
| E | Elongation factor tu-a | protein | 370 | 22% helix, 38% strand | Q88QP8 |
Ligands and binding sites
- GDP · Guanosine-5'-diphosphate · ligand · 5 copies · chains A, C, B, D, E
- MG · Magnesium ion · metal · 5 copies · chains A, B, C, D, E
- MPD · (4S)-2-methyl-2,4-pentanediol · additive · 5 copies · chains A, B, C, D, E
- MES · 2-(N-morpholino)-ethanesulfonic acid · additive · 3 copies · chains A, C, B, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 68 | 0.71 | 0.96 | 24 | empty |
| 2 | 295 | 0.53 | 0.75 | 28 | empty |
| 3 | 242 | 0.50 | 0.75 | 42 | empty |
| 4 | 147 | 0.50 | 0.79 | 18 | MES |
| 5 | 113 | 0.44 | 0.78 | 20 | MPD |
Interfaces
6 interfaces between chains.
- A–B · 849 Ų buried · 7 hydrogen bonds · protein-protein
- A–C · 222 Ų buried · 8 hydrogen bonds · protein-protein
- B–D · 206 Ų buried · 4 hydrogen bonds · protein-protein
- C–E · 202 Ų buried · 4 hydrogen bonds · protein-protein
- B–C · 123 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 4J0Q · Crystal structure of Pseudomonas putida elongation factor Tu (EF-Tu) · the same entry in another collection · chain C against C, TM-score 1.00
- Q88QP8 · AlphaFold monomer V2.0 prediction for elongation factor tu-a (Q88QP8) · a predicted model of the same protein · chain E against A, TM-score 0.59
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 Q88QP8
- Elsewhere: RCSB PDB 4J0Q · PDBe 4J0Q · UniProt Q88QP8
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