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Crystal structure of reconstructed bacterial elongation factor node 168
Analyse Crystal structure of reconstructed bacterial elongation factor node 168 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5W75
- Type
- protein
- Length
- 1,543 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Elongation factor tu
- UniProt
- B9K884
- Ligands
- GDP, GLC, FRU, MG, SO4
- Pockets
- 15 · best druggability 0.76
Structure
x-ray diffraction · 3 distinct chains · 22% helix, 39% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Elongation factor tu | protein | 384 | 22% helix, 39% strand | B9K884 |
| B | Elongation factor tu | protein | 385 | 23% helix, 39% strand | B9K884 |
| C, D | Elongation factor tu | protein | 387 | 21% helix, 39% strand | B9K884 |
Ligands and binding sites
- GDP · Guanosine-5'-diphosphate · ligand · 4 copies · chains A, B, C, D
- GLC · alpha-D-glucopyranose · sugar · 4 copies · chains B, D, C
- FRU · beta-D-fructofuranose · sugar · 4 copies · chains B, C, D
- MG · Magnesium ion · metal · 4 copies · chains A, B, C, D
- SO4 · Sulfate ion · ion · 21 copies · chains A, B, D, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 897 | 0.76 | 0.79 | 79 | GLC, FRU, SO4 |
| 2 | 449 | 0.71 | 0.81 | 32 | GLC, FRU, SO4 |
| 3 | 486 | 0.65 | 0.77 | 43 | empty |
| 4 | 232 | 0.51 | 0.76 | 35 | GDP, MG |
| 5 | 166 | 0.45 | 0.76 | 21 | SO4 |
Interfaces
3 interfaces between chains.
- B–D · 1456 Ų buried · 27 hydrogen bonds · protein-protein
- A–B · 669 Ų buried · 14 hydrogen bonds · protein-protein
- B–C · 381 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 5W75 · Crystal Structure of Reconstructed Bacterial Elongation Factor Node 168 · the same entry in another collection · chain D against D, TM-score 1.00
- B9K884 · AlphaFold monomer V2.0 prediction for elongation factor tu (B9K884) · a predicted model of the same protein · chain A 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 B9K884
- Elsewhere: RCSB PDB 5W75 · PDBe 5W75 · UniProt B9K884
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