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Structure of GLNK1 with bound effectors indicates regulatory mechanism for ammonia uptake

Analyse Structure of GLNK1 with bound effectors indicates regulatory mechanism for… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 2J9C
Type: protein
Length: 351 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Hypothetical nitrogen regulatory pii-like protein MJ0059
UniProt: Q60381
Ligands: ATP, MG, CL
Pockets: 3 · best druggability 0.78

Structure

x-ray diffraction · 1 distinct chain · 27% helix, 38% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C	Hypothetical nitrogen regulatory pii-like protein MJ0059	protein	117	27% helix, 38% strand	Q60381

Ligands and binding sites

ATP · Adenosine-5'-triphosphate · ligand · 3 copies · chains A, C, B
MG · Magnesium ion · metal · 3 copies · chains A, B, C
CL · Chloride ion · ion · 4 copies · chains A, B, C
EDO · 1,2-ethanediol · additive · 4 copies · chains A, C, B
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	355	0.78	0.88	47	ATP, MG, EDO
2	364	0.76	0.86	48	ATP, MG
3	363	0.76	0.86	53	ATP, MG, CL

Interfaces

3 interfaces between chains.

A–C · 1427 Å² buried · 25 hydrogen bonds · protein-protein
B–C · 1424 Å² buried · 28 hydrogen bonds · protein-protein
A–B · 1321 Å² buried · 24 hydrogen bonds · protein-protein

Compared structures

2J9C · Structure of GlnK1 with bound effectors indicates regulatory mechanism for ammonia uptake · the same entry in another collection · chain A against A, TM-score 1.00
Q60381 · AlphaFold monomer V2.0 prediction for uncharacterized nitrogen regulatory pii-like… · a predicted model of the same protein · chain A against A, TM-score 0.84

Analyse

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Every structure of UniProt Q60381
Elsewhere: RCSB PDB 2J9C · PDBe 2J9C · UniProt Q60381

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