Research workbench
Crystal structure of legionella effector sded (LPG2509) H67A in complex with ADP-ribosylated ubiquitin
Analyse Crystal structure of legionella effector sded (LPG2509) H67A in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6B7O
- Type
- protein
- Length
- 465 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Sded (LPG2509) H67A; Polyubiquitin-C
- UniProt
- Q5ZSK8, P0CG48
- Ligands
- AR6
- Pockets
- 5 · best druggability 0.65
Structure
x-ray diffraction · 2 distinct chains · 49% helix, 10% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Sded (LPG2509) H67A | protein | 313 | 55% helix, 4% strand | Q5ZSK8 |
| B, C | Polyubiquitin-C | protein | 76 | 24% helix, 32% strand | P0CG48 |
Ligands and binding sites
- AR6 · [(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-dihydroxy-oxolan-2-yl]methyl [hydroxy-[[(2R,3S,4R,5S)-3,4,5-trihydroxyoxolan-2-yl]methoxy]phosphoryl] hydrogen phosphate · ligand · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 444 | 0.65 | 0.78 | 45 | AR6 |
| 2 | 56 | 0.57 | 0.90 | 18 | empty |
| 3 | 120 | 0.48 | 0.79 | 20 | empty |
| 4 | 124 | 0.44 | 0.77 | 19 | empty |
| 5 | 71 | 0.40 | 0.80 | 15 | empty |
Interfaces
2 interfaces between chains.
- A–B · 1459 Ų buried · 18 hydrogen bonds · protein-protein
- A–C · 805 Ų buried · 17 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 6B7O · Crystal structure of Legionella effector sdeD (lpg2509) H67A in complex with… · 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 Q5ZSK8
- Every structure of UniProt P0CG48
- Elsewhere: RCSB PDB 6B7O · PDBe 6B7O · UniProt Q5ZSK8 · UniProt P0CG48
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.