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GLNK2 from archaeoglobus fulgidus, ATP complex

Analyse GLNK2 from archaeoglobus fulgidus, ATP complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3NCQ
Type: protein
Length: 339 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Nitrogen regulatory protein P-II (glnb-2)
UniProt: O28527
Ligands: ATP, MG, PO4, CL
Pockets: 3 · best druggability 0.74

Structure

x-ray diffraction · 2 distinct chains · 25% helix, 34% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Nitrogen regulatory protein P-II (glnb-2)	protein	112	25% helix, 35% strand	O28527
C	Nitrogen regulatory protein P-II (glnb-2)	protein	115	24% helix, 34% strand	O28527

Ligands and binding sites

ATP · Adenosine-5'-triphosphate · ligand · 3 copies · chains A, B, C
MG · Magnesium ion · metal · 3 copies · chains A, B, C
PO4 · Phosphate ion · ion · 2 copies · chains C, B
CL · Chloride ion · ion · chains A, B, C
ACT · Acetate ion · additive · 3 copies · chains A, B, C

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

Pockets

3 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	320	0.74	0.86	38	ATP, MG, PO4
2	351	0.72	0.84	39	ATP, MG
3	333	0.70	0.83	39	ATP, MG

Interfaces

3 interfaces between chains.

B–C · 1343 Å² buried · 25 hydrogen bonds · protein-protein
A–C · 1333 Å² buried · 27 hydrogen bonds · protein-protein
A–B · 1321 Å² buried · 24 hydrogen bonds · protein-protein

Compared structures

3NCQ · GlnK2 from Archaeoglobus fulgidus, ATP complex · the same entry in another collection · chain B against B, TM-score 1.00
O28527 · AlphaFold monomer V2.0 prediction for nitrogen regulatory protein GLNK2 (O28527) · a predicted model of the same protein · chain A against A, TM-score 0.89

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 O28527
Elsewhere: RCSB PDB 3NCQ · PDBe 3NCQ · UniProt O28527

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