Research workbench
Crystal structure of NikZ from Campylobacter jejuni in complex with Ni(L-His)
Analyse Crystal structure of NikZ from Campylobacter jejuni in complex with Ni(L-His) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4OEU
- Type
- protein
- Length
- 986 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.2
- Source
- Campylobacter jejuni
- Molecule
- Putative peptide ABC-transport system periplasmic peptide-binding protein
- UniProt
- Q0P844
- Ligands
- HIS, NI, MG
- Pockets
- 9 · best druggability 0.85
Structure
x-ray diffraction · resolution 2.2 · 1 distinct chain · 28% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Putative peptide ABC-transport system periplasmic peptide-binding protein | protein | 493 | 28% helix, 25% strand | Q0P844 |
Ligands and binding sites
- HIS · Histidine · ligand · 2 copies · chains A, B
- NI · Nickel (II) ion · metal · 3 copies · chains A, B
- MG · Magnesium ion · metal · 2 copies · chains A, B
- PEG · Di(hydroxyethyl)ether · additive · 3 copies · chains A, B
- GOL · Glycerol · additive · 3 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 306 | 0.85 | 0.95 | 47 | MG |
| 2 | 295 | 0.84 | 0.95 | 47 | MG |
| 3 | 164 | 0.79 | 0.95 | 38 | empty |
| 4 | 265 | 0.76 | 0.89 | 38 | empty |
| 5 | 524 | 0.69 | 0.79 | 43 | empty |
Interfaces
1 interface between chains.
- A–B · 185 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 4OEU · Crystal structure of nikz from campylobacter jejuni in complex with NI(L-his) · 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 Q0P844
- Elsewhere: RCSB PDB 4OEU · PDBe 4OEU · UniProt Q0P844
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