MolNFT v1 · #129527 · protein

Crystal structure of nika in complex with fe-L2 (N-(2-hydroxy- 3METHOXYBENZYL)-N-N'-ethylenediaminediacetic acid)

5ON0 · Nickel-binding periplasmic protein: “Crystal structure of nika in complex with fe-L2 (N-(2-hydroxy- 3METHOXYBENZYL)-N-N'-ethylenediaminediacetic…”. X-ray diffraction, 4 ligands (9YH, FE, CL), 6 pockets (best druggability 0.89).…

PDB: 5ON0
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: 9YH, FE, CL, SO4
Pockets: 6 · 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	31% helix, 25% strand	P33590
B	Nickel-binding periplasmic protein	protein	498	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 · 4 copies · chains A, B
SO4 · Sulfate ion · ion · chains A
GOL · Glycerol · additive · 13 copies · chains A, B
ACT · Acetate ion · additive · 9 copies · chains A, B

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

Pockets

6 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1028	0.89	0.90	141	GOL
2	1012	0.78	0.80	68	FE, 9YH, GOL, CL
3	1076	0.77	0.79	66	FE, 9YH, GOL, CL
4	929	0.77	0.80	68	empty
5	92	0.61	0.88	25	empty

Interfaces

1 interface between chains.

A–B · 1524 Å² buried · 19 hydrogen bonds · protein-protein

Compared structures

5ON0 · Crystal structure of NikA in complex with Fe-L2… · 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 5ON0 · PDBe 5ON0 · UniProt P33590

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