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B. subtilis glutamine synthetase structures reveal large active site conformational changes and basis for isoenzyme specific regulation: structure of the transition state complex

Analyse B. subtilis glutamine synthetase structures reveal large active site… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4LNI
Type: protein
Length: 5,314 residues
Chains: 12
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Glutamine synthetase
EC: 6.3.1.2
UniProt: P12425
Ligands: P3S, ADP, MG
Pockets: 20 · best druggability 0.81

Structure

x-ray diffraction · 2 distinct chains · 41% helix, 23% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D, E, F, G, H, I, K, L	Glutamine synthetase (EC 6.3.1.2)	protein	443	41% helix, 24% strand	P12425
J	Glutamine synthetase (EC 6.3.1.2)	protein	441	41% helix, 22% strand	P12425

Ligands and binding sites

P3S · L-methionine-S-sulfoximine phosphate · ligand · 12 copies · chains A, B, C, D, E, F, G, L, H, I, J, K
ADP · Adenosine-5'-diphosphate · ligand · 12 copies · chains A, B, C, D, E, F, G, L, H, I, J, K
MG · Magnesium ion · metal · 36 copies · chains A, B, C, D, E, F, G, H, I, J, K, L

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

Pockets

20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	431	0.81	0.90	55	P3S, ADP, MG
2	424	0.81	0.90	53	P3S, ADP, MG
3	464	0.81	0.89	57	P3S, ADP, MG
4	442	0.81	0.89	55	P3S, ADP, MG
5	438	0.81	0.89	57	P3S, ADP, MG

Interfaces

24 interfaces between chains.

F–L · 2108 Å² buried · 20 hydrogen bonds · protein-protein
A–G · 2108 Å² buried · 23 hydrogen bonds · protein-protein
E–K · 2099 Å² buried · 25 hydrogen bonds · protein-protein
B–H · 2092 Å² buried · 21 hydrogen bonds · protein-protein
D–J · 2086 Å² buried · 24 hydrogen bonds · protein-protein

Compared structures

4LNI · B. subtilis glutamine synthetase structures reveal large active site conformational… · the same entry in another collection · chain G against G, TM-score 1.00

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 P12425
Elsewhere: RCSB PDB 4LNI · PDBe 4LNI · UniProt P12425

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