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X-ray structure of nika in complex with ni-(L-HIS)2

Analyse X-ray structure of nika in complex with ni-(L-HIS)2 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4I8C
Type: protein
Length: 1,494 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Nickel-binding periplasmic protein
UniProt: P33590
Ligands: HIS, NI, SO4, CL
Pockets: 13 · best druggability 0.86

Structure

x-ray diffraction · 3 distinct chains · 31% helix, 24% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Nickel-binding periplasmic protein	protein	499	31% helix, 23% strand	P33590
B	Nickel-binding periplasmic protein	protein	499	31% helix, 22% strand	P33590
C	Nickel-binding periplasmic protein	protein	496	31% helix, 25% strand	P33590

Ligands and binding sites

HIS · Histidine · ligand · 6 copies · chains A, B, C
NI · Nickel (II) ion · metal · 3 copies · chains A, B, C
SO4 · Sulfate ion · ion · 2 copies · chains B, C
CL · Chloride ion · ion · chains B
ACT · Acetate ion · additive · 16 copies · chains A, B, C
GOL · Glycerol · additive · 8 copies · chains A, B, C

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

Pockets

13 pockets found on a 1 Å grid, 13 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	490	0.86	0.92	46	HIS, NI, ACT
2	510	0.86	0.92	50	HIS, NI, GOL, SO4
3	951	0.86	0.87	118	GOL
4	1000	0.82	0.83	74	HIS, NI, ACT, GOL
5	116	0.68	0.90	27	empty

Interfaces

2 interfaces between chains.

A–B · 1409 Å² buried · 18 hydrogen bonds · protein-protein
B–C · 706 Å² buried · 12 hydrogen bonds · protein-protein

Compared structures

4I8C · X-ray structure of NikA in complex with Ni-(L-His)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 0.88

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 4I8C · PDBe 4I8C · UniProt P33590

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