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Crystal structure of mutant nika

Analyse Crystal structure of mutant nika in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 2NOO
Type: protein
Length: 496 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Nickel-binding periplasmic protein
EC: 3.6.3.24
UniProt: P33590
Ligands: NI, IOD
Pockets: 4 · best druggability 0.72

Structure

x-ray diffraction · 1 distinct chain · 32% helix, 23% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Nickel-binding periplasmic protein (EC 3.6.3.24)	protein	496	32% helix, 23% strand	P33590

Ligands and binding sites

NI · Nickel (II) ion · metal · chains A
IOD · Iodide ion · ion · 2 copies · chains A

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

Pockets

4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	892	0.72	0.77	79	empty
2	169	0.69	0.88	29	empty
3	129	0.54	0.82	30	IOD
4	99	0.46	0.79	18	empty

Modifications

Observed in the structure: 2 modified (nonstandard).

Compared structures

2NOO · Crystal Structure of Mutant NikA · 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 0.97

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 2NOO · PDBe 2NOO · UniProt P33590

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