MolNFT v1 · #79667 · protein

A. fulgidus GLNK3, mgatp complex

3TA0 · Nitrogen regulatory protein P-II (glnb-3): “A. fulgidus GLNK3, mgatp complex”. X-ray diffraction, 1 ligand (ATP), 7 pockets (best druggability 0.77). MolNFT v1 #79667 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 3TA0
Type: protein
Length: 586 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Nitrogen regulatory protein P-II (glnb-3)
UniProt: O28524
Ligands: ATP
Pockets: 7 · best druggability 0.77

Structure

x-ray diffraction · 4 distinct chains · 29% helix, 40% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Nitrogen regulatory protein P-II (glnb-3)	protein	97	29% helix, 40% strand	O28524
B, E	Nitrogen regulatory protein P-II (glnb-3)	protein	97	29% helix, 41% strand	O28524
C	Nitrogen regulatory protein P-II (glnb-3)	protein	99	28% helix, 40% strand	O28524
D, F	Nitrogen regulatory protein P-II (glnb-3)	protein	98	29% helix, 40% strand	O28524

Ligands and binding sites

ATP · Adenosine-5'-triphosphate · ligand · 6 copies · chains A, B, C, D, E, F

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

Pockets

7 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1019	0.77	0.79	87	ATP
2	261	0.65	0.82	36	ATP
3	286	0.64	0.81	39	ATP
4	303	0.63	0.80	40	ATP
5	274	0.62	0.80	39	ATP

Interfaces

9 interfaces between chains.

A–C · 1276 Å² buried · 24 hydrogen bonds · protein-protein
E–F · 1247 Å² buried · 22 hydrogen bonds · protein-protein
D–E · 1230 Å² buried · 21 hydrogen bonds · protein-protein
D–F · 1226 Å² buried · 26 hydrogen bonds · protein-protein
B–C · 1226 Å² buried · 20 hydrogen bonds · protein-protein

Compared structures

3TA0 · A. fulgidus GlnK3, MgATP complex · the same entry in another collection · chain F against F, TM-score 1.00
O28524 · AlphaFold monomer V2.0 prediction for nitrogen regulatory protein GLNK3 (O28524) · 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 O28524
Elsewhere: RCSB PDB 3TA0 · PDBe 3TA0 · UniProt O28524

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