Research workbench
Structure of a Legionella effector with its substrate
Analyse Structure of a Legionella effector with its substrate in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5YIK
- Type
- protein
- Length
- 1,184 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 3.102
- Source
- Homo sapiens; Legionella pneumophila
- Molecule
- SdeA; ubiquitin
- UniProt
- Q6RCR0, P0CG47
- Pockets
- 16 · best druggability 0.74
Structure
x-ray diffraction · resolution 3.102 · 4 distinct chains · 48% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | SdeA | protein | 959 | 55% helix, 9% strand | Q6RCR0 |
| C | ubiquitin | protein | 71 | 15% helix, 30% strand | P0CG47 |
| D | ubiquitin | protein | 76 | 16% helix, 32% strand | P0CG47 |
| F | ubiquitin | protein | 78 | 24% helix, 36% strand | P0CG47 |
Pockets
16 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 152 | 0.74 | 0.91 | 31 | empty |
| 2 | 744 | 0.71 | 0.78 | 66 | empty |
| 3 | 512 | 0.68 | 0.79 | 60 | empty |
| 4 | 364 | 0.60 | 0.76 | 43 | empty |
| 5 | 181 | 0.56 | 0.80 | 23 | empty |
Interfaces
3 interfaces between chains.
- A–D · 1049 Ų buried · 13 hydrogen bonds · protein-protein
- A–F · 645 Ų buried · 5 hydrogen bonds · protein-protein
- A–C · 444 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 5YIK · Structure of a legionella effector with its substrate · the same entry in another collection · chain A against A, TM-score 1.00
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 Q6RCR0
- Every structure of UniProt P0CG47
- Elsewhere: RCSB PDB 5YIK · PDBe 5YIK · UniProt Q6RCR0 · UniProt P0CG47
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