Research workbench
Crystal structure of the virulence factor YopN in complex with its heterodimeric chaperone SycN-YscB
Analyse Crystal structure of the virulence factor YopN in complex with its… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1XKP
- Type
- protein
- Length
- 478 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.7
- Source
- Yersinia pestis
- Molecule
- putative membrane-bound Yop targeting protein YopN; Chaperone protein sycN; Chaperone…
- UniProt
- P61380, Q56973
- Pockets
- 7 · best druggability 0.65
Structure
x-ray diffraction · resolution 1.7 · 3 distinct chains · 55% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | putative membrane-bound Yop targeting protein YopN | protein | 231 | 71% helix, 5% strand | — |
| B | Chaperone protein sycN | protein | 121 | 40% helix, 31% strand | P61380 |
| C | Chaperone protein yscB | protein | 126 | 40% helix, 29% strand | Q56973 |
Pockets
7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 393 | 0.65 | 0.79 | 35 | empty |
| 2 | 185 | 0.61 | 0.83 | 20 | empty |
| 3 | 404 | 0.60 | 0.76 | 43 | empty |
| 4 | 128 | 0.45 | 0.77 | 24 | empty |
| 5 | 96 | 0.37 | 0.75 | 23 | empty |
Interfaces
3 interfaces between chains.
- A–C · 1718 Ų buried · 22 hydrogen bonds · protein-protein
- B–C · 1184 Ų buried · 14 hydrogen bonds · protein-protein
- A–B · 956 Ų buried · 15 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 21 modified (methylation, nonstandard).
Compared structures
- 1XKP · Crystal structure of the virulence factor yopn in complex with its heterodimeric… · the same entry in another collection · chain A against A, TM-score 1.00
- P61380 · AlphaFold monomer V2.0 prediction for chaperone protein sycn (P61380) · a predicted model of the same protein · chain B against A, TM-score 0.96
- Q56973 · AlphaFold monomer V2.0 prediction for chaperone protein yscb (Q56973) · 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 P61380
- Every structure of UniProt Q56973
- Elsewhere: RCSB PDB 1XKP · PDBe 1XKP · UniProt P61380 · UniProt Q56973
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