MolNFT v1 · #79668 · protein

A. fulgidus GLNK3, mgadp complex

3TA1 · Nitrogen regulatory protein P-II (glnb-3): “A. fulgidus GLNK3, mgadp complex”. X-ray diffraction, 1 ligand (ADP), 8 pockets (best druggability 0.69). MolNFT v1 #79668 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 3TA1
Type: protein
Length: 658 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: ADP
Pockets: 8 · best druggability 0.69

Structure

x-ray diffraction · 5 distinct chains · 25% helix, 36% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Nitrogen regulatory protein P-II (glnb-3)	protein	110	25% helix, 36% strand	O28524
B, F	Nitrogen regulatory protein P-II (glnb-3)	protein	112	25% helix, 36% strand	O28524
C	Nitrogen regulatory protein P-II (glnb-3)	protein	103	27% helix, 37% strand	O28524
D	Nitrogen regulatory protein P-II (glnb-3)	protein	115	24% helix, 35% strand	O28524
E	Nitrogen regulatory protein P-II (glnb-3)	protein	106	26% helix, 38% strand	O28524

Ligands and binding sites

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

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	210	0.69	0.86	35	ADP
2	224	0.69	0.86	40	ADP
3	208	0.69	0.86	40	ADP
4	200	0.69	0.86	36	ADP
5	217	0.68	0.85	34	ADP

Interfaces

8 interfaces between chains.

E–F · 1254 Å² buried · 22 hydrogen bonds · protein-protein
B–F · 1243 Å² buried · 25 hydrogen bonds · protein-protein
A–D · 1237 Å² buried · 24 hydrogen bonds · protein-protein
C–D · 1235 Å² buried · 23 hydrogen bonds · protein-protein
B–E · 1214 Å² buried · 23 hydrogen bonds · protein-protein

Compared structures

3TA1 · A. fulgidus GlnK3, MgADP 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 C against A, TM-score 0.94

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 3TA1 · PDBe 3TA1 · UniProt O28524

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