Research workbench
Crystal structure of nikr from helicobacter pylori with variable ni site coordination
Analyse Crystal structure of nikr from helicobacter pylori with variable ni site… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3LGH
- Type
- protein
- Length
- 427 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Nickel-responsive regulator
- UniProt
- O25896
- Ligands
- NI, MG
- Pockets
- 3 · best druggability 0.78
Structure
x-ray diffraction · 4 distinct chains · 36% helix, 38% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Nickel-responsive regulator | protein | 131 | 41% helix, 34% strand | O25896 |
| B | Nickel-responsive regulator | protein | 139 | 37% helix, 32% strand | O25896 |
| C | Nickel-responsive regulator | protein | 79 | 30% helix, 46% strand | O25896 |
| D | Nickel-responsive regulator | protein | 78 | 31% helix, 45% strand | O25896 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 844 | 0.78 | 0.81 | 81 | empty |
| 2 | 225 | 0.49 | 0.75 | 30 | empty |
| 3 | 56 | 0.42 | 0.81 | 12 | empty |
Interfaces
4 interfaces between chains.
- A–B · 1882 Ų buried · 20 hydrogen bonds · protein-protein
- A–C · 1072 Ų buried · 7 hydrogen bonds · protein-protein
- B–D · 900 Ų buried · 6 hydrogen bonds · protein-protein
- B–C · 49 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 3LGH · Crystal structure of NikR from Helicobacter pylori with variable Ni site coordination · the same entry in another collection · chain D against D, TM-score 1.00
- O25896 · AlphaFold monomer V2.0 prediction for putative nickel-responsive regulator (O25896) · a predicted model of the same protein · chain A against A, TM-score 0.95
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 3LGH · PDBe 3LGH · UniProt O25896
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