Research workbench
Nikr from helicobacter pylori in closed trans-conformation and nickel bound to 4 intermediary sites
Analyse Nikr from helicobacter pylori in closed trans-conformation and nickel bound to… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2CAJ
- Type
- protein
- Length
- 267 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative nickel-responsive regulator
- UniProt
- O25896
- Ligands
- NI, CL
- Pockets
- 1 · best druggability 0.69
Structure
x-ray diffraction · 2 distinct chains · 39% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Putative nickel-responsive regulator | protein | 128 | 39% helix, 33% strand | O25896 |
| B | Putative nickel-responsive regulator | protein | 139 | 38% helix, 31% strand | O25896 |
Ligands and binding sites
- NI · Nickel (II) ion · metal · 2 copies · chains B
- CL · Chloride ion · ion · chains 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
1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 617 | 0.69 | 0.78 | 55 | GOL |
Interfaces
1 interface between chains.
- A–B · 2729 Ų buried · 34 hydrogen bonds · protein-protein
Compared structures
- 2CAJ · NikR from Helicobacter pylori in closed trans-conformation and nickel bound to 4… · the same entry in another collection · chain A against A, TM-score 1.00
- O25896 · AlphaFold monomer V2.0 prediction for putative nickel-responsive regulator (O25896) · a predicted model of the same protein · chain B against A, TM-score 0.95
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 O25896
- Elsewhere: RCSB PDB 2CAJ · PDBe 2CAJ · UniProt O25896
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