Research workbench
Yersinia yscu C-terminal fragment in complex with a synthetic compound
Analyse Yersinia yscu C-terminal fragment in complex with a synthetic compound in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6EJP
- Type
- protein
- Length
- 281 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Yop proteins translocation protein U
- UniProt
- P69986
- Ligands
- B8E, NA, PO4, CL
- Pockets
- 1 · best druggability 0.58
Structure
x-ray diffraction · 4 distinct chains · 57% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Yop proteins translocation protein U | protein | 53 | 68% helix, 8% strand | P69986 |
| C | Yop proteins translocation protein U | protein | 87 | 51% helix, 20% strand | P69986 |
| B | Yop proteins translocation protein U | protein | 51 | 71% helix, 8% strand | P69986 |
| D | Yop proteins translocation protein U | protein | 90 | 49% helix, 19% strand | P69986 |
Ligands and binding sites
- B8E · methyl 2-(5-methyl-2-phenyl-1,3-thiazol-4-yl)ethanoate · ligand · 2 copies · chains C, D
- NA · Sodium ion · metal · chains A, C
- PO4 · Phosphate ion · ion · 3 copies · chains A, C, B
- CL · Chloride ion · ion · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 464 | 0.58 | 0.74 | 30 | B8E |
Interfaces
3 interfaces between chains.
- B–D · 1152 Ų buried · 24 hydrogen bonds · protein-protein
- A–C · 1139 Ų buried · 24 hydrogen bonds · protein-protein
- C–D · 376 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 6EJP · Yersinia YscU C-terminal fragment in complex with a synthetic compound · the same entry in another collection · chain D against D, TM-score 1.00
- P69986 · AlphaFold monomer V2.0 prediction for yop proteins translocation protein U (P69986) · a predicted model of the same protein · chain C against A, TM-score 0.95
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 P69986
- Elsewhere: RCSB PDB 6EJP · PDBe 6EJP · UniProt P69986
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.