Research workbench
Structural study of legionella pneumophila effector doty (LPG0294)
Analyse Structural study of legionella pneumophila effector doty (LPG0294) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7UPS
- Type
- protein
- Length
- 834 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Doty (LPG0294)
- UniProt
- Q5ZYR7
- Pockets
- 9 · best druggability 0.70
Structure
x-ray diffraction · 2 distinct chains · 51% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Doty (LPG0294) | protein | 215 | 52% helix, 15% strand | Q5ZYR7 |
| C, D | Doty (LPG0294) | protein | 202 | 50% helix, 16% strand | Q5ZYR7 |
Ligands and binding sites
- EDO · 1,2-ethanediol · additive · 4 copies · chains A, C, B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 439 | 0.70 | 0.81 | 41 | empty |
| 2 | 790 | 0.70 | 0.76 | 83 | empty |
| 3 | 445 | 0.67 | 0.79 | 45 | empty |
| 4 | 409 | 0.66 | 0.79 | 38 | empty |
| 5 | 395 | 0.60 | 0.76 | 50 | empty |
Interfaces
4 interfaces between chains.
- A–B · 998 Ų buried · 15 hydrogen bonds · protein-protein
- B–D · 611 Ų buried · 18 hydrogen bonds · protein-protein
- A–C · 526 Ų buried · 5 hydrogen bonds · protein-protein
- B–C · 95 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 7UPS · Structural study of Legionella pneumophila effector DotY (Lpg0294) · 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 Q5ZYR7
- Elsewhere: RCSB PDB 7UPS · PDBe 7UPS · UniProt Q5ZYR7
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