MolNFT v2 · #50483 · protein
Crystal structure of uncharacterized protein YdcJ (SF1787) from Shigella flexneri which includes domain DUF1338. Northeast Structural Genomics Consortium target SfR276
2RJB: “Crystal structure of uncharacterized protein YdcJ (SF1787) from Shigella flexneri which includes domain…”. X-ray diffraction at 2.6, 1 ligand (ZN), 20 pockets (best druggability 0.77). MolNFT v2 #50483 on GenesisL1: 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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