Research workbench
Structure of a legionella effector
Analyse Structure of a legionella effector in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5YIM
- Type
- protein
- Length
- 1,829 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Sdea
- UniProt
- Q6RCR0
- Pockets
- 20 · best druggability 0.82
Structure
x-ray diffraction · 2 distinct chains · 54% helix, 7% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Sdea | protein | 933 | 54% helix, 8% strand | Q6RCR0 |
| C | Sdea | protein | 896 | 54% helix, 6% strand | Q6RCR0 |
Pockets
20 pockets found on a 1 Å grid, 18 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1140 | 0.82 | 0.83 | 84 | empty |
| 2 | 458 | 0.72 | 0.81 | 42 | empty |
| 3 | 53 | 0.72 | 0.98 | 17 | empty |
| 4 | 674 | 0.71 | 0.78 | 67 | empty |
| 5 | 261 | 0.71 | 0.86 | 37 | empty |
Interfaces
1 interface between chains.
- A–C · 738 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 5YIM · Structure of a Legionella effector · 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
- Elsewhere: RCSB PDB 5YIM · PDBe 5YIM · UniProt Q6RCR0
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