Research workbench

Nickel binding domain of nikr from helicobacter pylori disclosing partial metal occupancy

Analyse Nickel binding domain of nikr from helicobacter pylori disclosing partial metal… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3QSI
Type: protein
Length: 795 residues
Chains: 10
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Nikr nickel-responsive regulator
UniProt: O25896
Ligands: NI, SO4
Pockets: 8 · best druggability 0.76

Structure

x-ray diffraction · 6 distinct chains · 30% helix, 44% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
B	Nikr nickel-responsive regulator	protein	81	30% helix, 40% strand	O25896
C, E	Nikr nickel-responsive regulator	protein	80	30% helix, 49% strand	O25896
D, G, J, I	Nikr nickel-responsive regulator	protein	79	30% helix, 42% strand	O25896
A	Nikr nickel-responsive regulator	protein	80	30% helix, 48% strand	O25896
F	Nikr nickel-responsive regulator	protein	78	31% helix, 42% strand	O25896
H	Nikr nickel-responsive regulator	protein	80	30% helix, 41% strand	O25896

Ligands and binding sites

NI · Nickel (II) ion · metal · 9 copies · chains B, A, C, D, F, E, G, H, I
SO4 · Sulfate ion · ion · 5 copies · chains B, C, F, G, H, E

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

8 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	324	0.76	0.88	58	empty
2	132	0.74	0.93	32	SO4
3	116	0.73	0.93	26	empty
4	866	0.72	0.77	72	SO4
5	94	0.38	0.76	18	empty

Interfaces

17 interfaces between chains.

C–D · 855 Å² buried · 19 hydrogen bonds · protein-protein
B–A · 828 Å² buried · 14 hydrogen bonds · protein-protein
G–H · 826 Å² buried · 18 hydrogen bonds · protein-protein
F–E · 826 Å² buried · 19 hydrogen bonds · protein-protein
H–E · 792 Å² buried · 2 hydrogen bonds · protein-protein

Compared structures

3QSI · Nickel binding domain of NikR from Helicobacter pylori disclosing partial metal occupancy · the same entry in another collection · chain I against I, TM-score 1.00
O25896 · AlphaFold monomer V2.0 prediction for putative nickel-responsive regulator (O25896) · a predicted model of the same protein · chain C against A, TM-score 0.98

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 3QSI · PDBe 3QSI · UniProt O25896

GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.