MolNFT v1 · #102204 · protein
Crystal structure of nikz from campylobacter jejuni in complex with NI(II) ion
4OEV · Putative peptide ABC-transport system periplasmic peptide…: “Crystal structure of nikz from campylobacter jejuni in complex with NI(II) ion”. X-ray diffraction, 2 ligands (OXL, NI), 10 pockets (best druggability 0.84). MolNFT v1…
- 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
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