MolNFT v1 · #129531 · protein

Crystal structure of nika in complex with fe-L1 (N-(2-hydroxybenzyl)- N'-(2-thiomethylbenzyl)-N,N'-ethylenediamine diacetic acid)

5ON4 · Nickel-binding periplasmic protein: “Crystal structure of nika in complex with fe-L1 (N-(2-hydroxybenzyl)…”. X-ray diffraction, 2 ligands (9YK, FE), 6 pockets (best druggability 0.89). MolNFT v1 #129531 on GenesisL1: 3D structure…

PDB: 5ON4
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: 9YK, FE
Pockets: 6 · best druggability 0.89

Structure

x-ray diffraction · 1 distinct chain · 31% helix, 25% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Nickel-binding periplasmic protein	protein	498	31% helix, 25% strand	P33590

Ligands and binding sites

9YK · 2-[2-[[2,3-bis(oxidanyl)phenyl]methyl-(2-hydroxy-2-oxoethyl)amino]ethyl-[(2-methylsulfanylphenyl)methyl]amino]ethanoic acid · ligand · 2 copies · chains A, B
FE · Fe (III) ion · metal · 2 copies · chains A, B
GOL · Glycerol · additive · 4 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	1027	0.89	0.90	147	empty
2	1151	0.78	0.80	70	FE, 9YK, GOL
3	1009	0.77	0.79	69	FE, 9YK, GOL
4	195	0.70	0.88	38	empty
5	204	0.69	0.87	36	empty

Interfaces

1 interface between chains.

A–B · 1628 Å² buried · 20 hydrogen bonds · protein-protein

Compared structures

5ON4 · Crystal structure of NikA in complex with Fe-L1… · 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 5ON4 · PDBe 5ON4 · UniProt P33590

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