Research workbench
Histidine 416 of the periplamsic binding protein nika is essential for nickel uptake in escherichia COLI
Analyse Histidine 416 of the periplamsic binding protein nika is essential for nickel… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3QIM
- Type
- protein
- Length
- 996 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Nickel-binding periplasmic protein
- UniProt
- P33590
- Ligands
- SO4
- Pockets
- 7 · best druggability 0.89
Structure
x-ray diffraction · 2 distinct chains · 31% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Nickel-binding periplasmic protein | protein | 498 | 32% helix, 25% strand | P33590 |
| B | Nickel-binding periplasmic protein | protein | 498 | 31% helix, 24% strand | P33590 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 4 copies · chains A, B
- ACT · Acetate ion · additive · 13 copies · chains A, B
- GOL · Glycerol · additive · 8 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1171 | 0.89 | 0.90 | 154 | ACT |
| 2 | 1146 | 0.78 | 0.80 | 68 | GOL, ACT |
| 3 | 1056 | 0.78 | 0.80 | 69 | GOL, ACT, SO4 |
| 4 | 138 | 0.74 | 0.93 | 31 | empty |
| 5 | 58 | 0.55 | 0.89 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 1673 Ų buried · 24 hydrogen bonds · protein-protein
Compared structures
- 3QIM · Histidine 416 of the periplamsic binding protein NikA is essential for nickel uptake in… · the same entry in another collection · chain A against A, TM-score 1.00
- P33590 · AlphaFold monomer V2.0 prediction for nickel-binding periplasmic protein (P33590) · a predicted model of the same protein · chain A against A, TM-score 0.94
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 P33590
- Elsewhere: RCSB PDB 3QIM · PDBe 3QIM · UniProt P33590
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