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
- 2WVD
- Type
- protein
- Length
- 539 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative nickel-responsive regulator
- UniProt
- O25896
- Ligands
- SO4
- Pockets
- 5 · best druggability 0.78
Structure
x-ray diffraction · 4 distinct chains · 40% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Putative nickel-responsive regulator | protein | 133 | 40% helix, 33% strand | O25896 |
| B | Putative nickel-responsive regulator | protein | 135 | 41% helix, 32% strand | O25896 |
| C | Putative nickel-responsive regulator | protein | 133 | 38% helix, 34% strand | O25896 |
| D | Putative nickel-responsive regulator | protein | 138 | 42% helix, 30% strand | O25896 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 6 copies · chains A, B, C, D
- GOL · Glycerol · additive · 6 copies · chains A, D, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 526 | 0.78 | 0.85 | 72 | GOL |
| 2 | 820 | 0.77 | 0.81 | 65 | empty |
| 3 | 395 | 0.70 | 0.81 | 49 | GOL |
| 4 | 293 | 0.62 | 0.79 | 28 | empty |
| 5 | 165 | 0.55 | 0.81 | 19 | empty |
Interfaces
6 interfaces between chains.
- C–D · 3041 Ų buried · 37 hydrogen bonds · protein-protein
- A–B · 2966 Ų buried · 22 hydrogen bonds · protein-protein
- A–D · 607 Ų buried · 10 hydrogen bonds · protein-protein
- B–C · 429 Ų buried · 12 hydrogen bonds · protein-protein
- B–D · 51 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 2WVD · Structural and mechanistic insights into Helicobacter pylori NikR function · the same entry in another collection · chain C against C, 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 0.85
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 2WVD · PDBe 2WVD · UniProt O25896
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