MolNFT v1 · #33115 · protein
Nikr from helicobacter pylori in closed trans-conformation and nickel bound to 2F, 2X and 2I sites.
2CAD · Putative nickel-responsive regulator: “Nikr from helicobacter pylori in closed trans-conformation and nickel bound to 2F, 2X and 2I sites.”. X-ray diffraction, 1 ligand (NI), 2 pockets (best druggability 0.65). MolNFT v1 #33115 on…
- PDB
- 2CAD
- Type
- protein
- Length
- 265 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative nickel-responsive regulator
- UniProt
- O25896
- Ligands
- NI
- Pockets
- 2 · best druggability 0.65
Structure
x-ray diffraction · 2 distinct chains · 40% helix, 35% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Putative nickel-responsive regulator | protein | 131 | 40% helix, 37% strand | O25896 |
| B | Putative nickel-responsive regulator | protein | 134 | 40% helix, 34% strand | O25896 |
Ligands and binding sites
- NI · Nickel (II) ion · metal · 3 copies · chains A, B
- FMT · Formic acid · additive · 4 copies · chains A, B
- GOL · Glycerol · additive · 3 copies · chains A, B
- CIT · Citric acid · additive · chains 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 | 495 | 0.65 | 0.77 | 44 | FMT |
| 2 | 50 | 0.42 | 0.82 | 12 | GOL |
Interfaces
1 interface between chains.
- A–B · 2835 Ų buried · 34 hydrogen bonds · protein-protein
Compared structures
- 2CAD · NikR from Helicobacter pylori in closed trans-conformation and nickel bound to 2F, 2X and… · 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 0.97
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 2CAD · PDBe 2CAD · UniProt O25896
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