Research workbench
Nikr in closed conformation and nickel bound to high- affinity sites
Analyse Nikr in closed conformation and nickel bound to high- affinity sites in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2BJ7
- Type
- protein
- Length
- 274 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Nickel responsive regulator
- UniProt
- O58316
- Ligands
- NI, CL
- Pockets
- 2 · best druggability 0.67
Structure
x-ray diffraction · 2 distinct chains · 39% helix, 35% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Nickel responsive regulator | protein | 136 | 38% helix, 35% strand | O58316 |
| B | Nickel responsive regulator | protein | 138 | 41% helix, 35% strand | O58316 |
Ligands and binding sites
- NI · Nickel (II) ion · metal · 4 copies · chains A, B
- CL · Chloride ion · ion · chains A, B
- EDO · 1,2-ethanediol · additive · 2 copies · chains A, B
- PG4 · Tetraethylene glycol · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 344 | 0.67 | 0.81 | 38 | PG4 |
| 2 | 70 | 0.31 | 0.74 | 14 | empty |
Interfaces
1 interface between chains.
- A–B · 3398 Ų buried · 32 hydrogen bonds · protein-protein
Compared structures
- 2BJ7 · Nikr in closed conformation and nickel bound to high-affinity sites · the same entry in another collection · chain A against A, TM-score 1.00
- O58316 · AlphaFold monomer V2.0 prediction for putative nickel-responsive regulator (O58316) · a predicted model of the same protein · chain B against A, TM-score 0.96
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 O58316
- Elsewhere: RCSB PDB 2BJ7 · PDBe 2BJ7 · UniProt O58316
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