Research workbench
Structural and mechanistic insights into helicobacter pylori nikr function
Analyse Structural and mechanistic insights into helicobacter pylori nikr function in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2WVC
- Type
- protein
- Length
- 270 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative nickel-responsive regulator
- UniProt
- O25896
- Ligands
- SO4
- Pockets
- 2 · best druggability 0.73
Structure
x-ray diffraction · 2 distinct chains · 39% helix, 35% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Putative nickel-responsive regulator | protein | 132 | 38% helix, 35% strand | O25896 |
| B | Putative nickel-responsive regulator | protein | 138 | 39% helix, 35% strand | O25896 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 4 copies · chains A, B
- GOL · Glycerol · additive · 5 copies · chains A, B
- FMT · Formic acid · additive · 3 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 | 753 | 0.73 | 0.78 | 55 | GOL, FMT |
| 2 | 54 | 0.41 | 0.81 | 14 | GOL |
Interfaces
1 interface between chains.
- A–B · 2900 Ų buried · 41 hydrogen bonds · protein-protein
Compared structures
- 2WVC · Structural and mechanistic insights into Helicobacter pylori NikR function · 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 0.96
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 O25896
- Elsewhere: RCSB PDB 2WVC · PDBe 2WVC · UniProt O25896
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