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Crystal structure of uncharacterized protein YdcJ (SF1787) from Shigella flexneri which includes domain DUF1338. Northeast Structural Genomics Consortium target SfR276
Analyse Crystal structure of uncharacterized protein YdcJ (SF1787) from Shigella… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2RJB
- Type
- protein
- Length
- 1,572 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.6
- Source
- Shigella flexneri
- Molecule
- Uncharacterized protein
- UniProt
- Q83KU0
- Ligands
- ZN
- Pockets
- 20 · best druggability 0.77
Structure
x-ray diffraction · resolution 2.6 · 4 distinct chains · 47% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Uncharacterized protein | protein | 418 | 49% helix, 20% strand | Q83KU0 |
| B | Uncharacterized protein | protein | 418 | 48% helix, 18% strand | Q83KU0 |
| C | Uncharacterized protein | protein | 364 | 47% helix, 18% strand | Q83KU0 |
| D | Uncharacterized protein | protein | 372 | 42% helix, 18% strand | Q83KU0 |
Ligands and binding sites
- ZN · Zinc ion · metal · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 969 | 0.77 | 0.79 | 88 | ZN |
| 2 | 587 | 0.72 | 0.80 | 56 | ZN |
| 3 | 690 | 0.71 | 0.78 | 56 | ZN |
| 4 | 563 | 0.69 | 0.78 | 51 | ZN |
| 5 | 366 | 0.68 | 0.81 | 36 | empty |
Interfaces
3 interfaces between chains.
- A–B · 563 Ų buried · 6 hydrogen bonds · protein-protein
- C–D · 96 Ų buried · 1 hydrogen bond · protein-protein
- A–D · 69 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 39 modified (engineered).
Compared structures
- 2RJB · Crystal structure of uncharacterized protein ydcj (SF1787) from shigella flexneri which… · 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 Q83KU0
- Elsewhere: RCSB PDB 2RJB · PDBe 2RJB · UniProt Q83KU0
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