Research workbench
Crystal structure of nikz from campylobacter jejuni in complex with NI(II) ion
Analyse Crystal structure of nikz from campylobacter jejuni in complex with NI(II) ion in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4OEV
- Type
- protein
- Length
- 988 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative peptide ABC-transport system periplasmic peptide- binding protein
- UniProt
- Q0P844
- Ligands
- OXL, NI
- Pockets
- 10 · best druggability 0.84
Structure
x-ray diffraction · 1 distinct chain · 29% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Putative peptide ABC-transport system periplasmic peptide- binding protein | protein | 494 | 29% helix, 25% strand | Q0P844 |
Ligands and binding sites
- OXL · Oxalate ion · ligand · 2 copies · chains A, B
- NI · Nickel (II) ion · metal · 2 copies · chains A, B
- GOL · Glycerol · additive · 6 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 348 | 0.84 | 0.94 | 51 | empty |
| 2 | 357 | 0.84 | 0.93 | 48 | GOL |
| 3 | 877 | 0.84 | 0.86 | 95 | GOL |
| 4 | 153 | 0.81 | 0.97 | 36 | empty |
| 5 | 150 | 0.80 | 0.96 | 35 | empty |
Interfaces
1 interface between chains.
- A–B · 805 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 4OEV · Crystal structure of NikZ from Campylobacter jejuni in complex with Ni(II) ion · the same entry in another collection · chain B against B, 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 4OEV · PDBe 4OEV · UniProt Q0P844
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.