Research workbench
Structure of a legionella effector with substrates
Analyse Structure of a legionella effector with substrates in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5YIJ
- Type
- protein
- Length
- 1,183 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Sdea; Ubiquitin
- UniProt
- Q6RCR0, P0CG47
- Ligands
- NAI
- Pockets
- 16 · best druggability 0.73
Structure
x-ray diffraction · 4 distinct chains · 49% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Sdea | protein | 959 | 56% helix, 9% strand | Q6RCR0 |
| C | Ubiquitin | protein | 71 | 17% helix, 31% strand | P0CG47 |
| D | Ubiquitin | protein | 76 | 25% helix, 32% strand | P0CG47 |
| G | Ubiquitin | protein | 77 | 19% helix, 38% strand | P0CG47 |
Ligands and binding sites
- NAI · 1,4-dihydronicotinamide adenine dinucleotide · ligand · chains A, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
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 | 775 | 0.73 | 0.78 | 67 | NAI |
| 2 | 130 | 0.70 | 0.90 | 27 | empty |
| 3 | 475 | 0.67 | 0.78 | 52 | empty |
| 4 | 476 | 0.61 | 0.75 | 49 | empty |
| 5 | 183 | 0.55 | 0.80 | 22 | empty |
Interfaces
3 interfaces between chains.
- A–D · 1064 Ų buried · 12 hydrogen bonds · protein-protein
- A–G · 671 Ų buried · 7 hydrogen bonds · protein-protein
- A–C · 417 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 5YIJ · Structure of a Legionella effector with substrates · 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 5YIJ · PDBe 5YIJ · UniProt Q6RCR0 · UniProt P0CG47
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.