Research workbench

GLNK2 from archaeoglubus fulgidus, ADP complex

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

PDB: 3NCR
Type: protein
Length: 341 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: ADP, MG, PO4, CL
Pockets: 3 · best druggability 0.74

Structure

x-ray diffraction · 3 distinct chains · 25% helix, 37% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Nitrogen regulatory protein P-II (glnb-2)	protein	113	25% helix, 38% strand	O28527
B	Nitrogen regulatory protein P-II (glnb-2)	protein	112	25% helix, 37% strand	O28527
C	Nitrogen regulatory protein P-II (glnb-2)	protein	116	24% helix, 37% strand	O28527

Ligands and binding sites

ADP · Adenosine-5'-diphosphate · ligand · 3 copies · chains A, B, C
MG · Magnesium ion · metal · 3 copies · chains A, B, C
PO4 · Phosphate ion · ion · 4 copies · chains A, B, C
CL · Chloride ion · ion · chains A, B, C
ACT · Acetate ion · additive · 2 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	377	0.74	0.85	43	ADP, PO4, MG, ACT
2	262	0.71	0.85	38	ADP, MG
3	343	0.69	0.82	37	ADP, MG, ACT

Interfaces

3 interfaces between chains.

A–C · 1357 Å² buried · 26 hydrogen bonds · protein-protein
B–C · 1350 Å² buried · 23 hydrogen bonds · protein-protein
A–B · 1346 Å² buried · 24 hydrogen bonds · protein-protein

Compared structures

3NCR · GlnK2 from Archaeoglubus fulgidus, ADP 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 B against A, TM-score 0.88

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 3NCR · PDBe 3NCR · UniProt O28527

GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.