Research workbench
Crystal structure of NikA in complex with reduced Fe-L1 (N-(2-hydroxybenzyl)-N'-(2-thiomethylbenzyl)-N,N'-ethylenediamine diacetic acid)
Analyse Crystal structure of NikA in complex with reduced Fe-L1… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5ON9
- Type
- protein
- Length
- 995 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.7
- Source
- Escherichia coli (strain K12)
- Molecule
- Nickel-binding periplasmic protein
- UniProt
- P33590
- Ligands
- 9YH, FE, CL
- Pockets
- 5 · best druggability 0.89
Structure
x-ray diffraction · resolution 1.7 · 2 distinct chains · 31% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Nickel-binding periplasmic protein | protein | 498 | 31% helix, 25% strand | P33590 |
| B | Nickel-binding periplasmic protein | protein | 497 | 31% helix, 24% strand | P33590 |
Ligands and binding sites
- 9YH · 2-[2-[2-hydroxy-2-oxoethyl-[(3-methoxy-2-oxidanyl-phenyl)methyl]amino]ethyl-[(2-methylsulfanylphenyl)methyl]amino]ethanoic acid · ligand · 2 copies · chains A, B
- FE · Fe (III) ion · metal · 2 copies · chains A, B
- CL · Chloride ion · ion · chains A
- GOL · Glycerol · additive · 9 copies · chains A, B
- ACT · Acetate ion · additive · 5 copies · chains A, B
- DTT · 2,3-dihydroxy-1,4-dithiobutane · additive · 2 copies · chains A, B
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 | 1058 | 0.89 | 0.90 | 149 | GOL |
| 2 | 997 | 0.79 | 0.80 | 85 | empty |
| 3 | 1101 | 0.78 | 0.79 | 66 | FE, 9YH, GOL, DTT |
| 4 | 1118 | 0.76 | 0.78 | 68 | FE, 9YH, DTT, GOL, ACT |
| 5 | 78 | 0.54 | 0.86 | 23 | empty |
Interfaces
1 interface between chains.
- A–B · 1567 Ų buried · 20 hydrogen bonds · protein-protein
Compared structures
- 5ON9 · Crystal structure of nika in complex with reduced fe-L1 (N-(2… · 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 5ON9 · PDBe 5ON9 · UniProt P33590
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