Research workbench
Crystal structure of hypb from helicobacter pylori in complex with nickel
Analyse Crystal structure of hypb from helicobacter pylori in complex with nickel in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4LPS
- Type
- protein
- Length
- 430 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- HYDROGENASE/UREASE nickel incorporation protein hypb
- UniProt
- O25560
- Ligands
- GDP, MG, NI, PO4
- Pockets
- 3 · best druggability 0.65
Structure
x-ray diffraction · 1 distinct chain · 42% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | HYDROGENASE/UREASE nickel incorporation protein hypb | protein | 215 | 42% helix, 18% strand | O25560 |
Ligands and binding sites
- GDP · Guanosine-5'-diphosphate · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 2 copies · chains A, B
- NI · Nickel (II) ion · metal · chains A, B
- PO4 · Phosphate ion · ion · 5 copies · chains A, B
- GOL · Glycerol · additive · 7 copies · chains A, B
- MLI · Malonate ion · additive · 3 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 272 | 0.65 | 0.82 | 41 | MG, GDP, PO4 |
| 2 | 251 | 0.63 | 0.82 | 42 | MG, GDP, PO4 |
| 3 | 55 | 0.29 | 0.75 | 15 | GOL |
Interfaces
1 interface between chains.
- A–B · 1324 Ų buried · 12 hydrogen bonds · protein-protein
Compared structures
- 4LPS · Crystal structure of HypB from Helicobacter pylori in complex with nickel · the same entry in another collection · chain A against A, TM-score 1.00
- O25560 · AlphaFold monomer V2.0 prediction for HYDROGENASE/UREASE maturation factor hypb (O25560) · a predicted model of the same protein · chain A against A, TM-score 1.00
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 O25560
- Elsewhere: RCSB PDB 4LPS · PDBe 4LPS · UniProt O25560
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