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B. subtilis glutamine synthetase structures reveal large active site conformational changes and basis for isoenzyme specific regulation: structure of gs-glutamate-amppcp 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
- 4LNK
- Type
- protein
- Length
- 2,658 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glutamine synthetase
- EC
- 6.3.1.2
- UniProt
- P12425
- Ligands
- GLU, ADP, MG, SO4
- Pockets
- 20 · best druggability 0.81
Structure
x-ray diffraction · 1 distinct chain · 37% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F | Glutamine synthetase (EC 6.3.1.2) | protein | 443 | 37% helix, 22% strand | P12425 |
Ligands and binding sites
- GLU · Glutamic acid · ligand · 6 copies · chains A, B, C, D, E, F
- ADP · Adenosine-5'-diphosphate · ligand · 6 copies · chains A, B, C, D, E, F
- MG · Magnesium ion · metal · 12 copies · chains A, B, C, D, E, F
- SO4 · Sulfate ion · ion · 3 copies · chains A, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 492 | 0.81 | 0.88 | 59 | GLU, ADP, MG |
| 2 | 423 | 0.80 | 0.89 | 51 | GLU, ADP, MG |
| 3 | 420 | 0.80 | 0.88 | 57 | GLU, ADP, MG |
| 4 | 441 | 0.79 | 0.88 | 63 | GLU, ADP, MG |
| 5 | 388 | 0.79 | 0.88 | 54 | GLU, ADP, MG |
Interfaces
6 interfaces between chains.
- A–F · 1836 Ų buried · 37 hydrogen bonds · protein-protein
- D–E · 1832 Ų buried · 28 hydrogen bonds · protein-protein
- A–B · 1820 Ų buried · 34 hydrogen bonds · protein-protein
- E–F · 1812 Ų buried · 33 hydrogen bonds · protein-protein
- B–C · 1791 Ų buried · 36 hydrogen bonds · protein-protein
Compared structures
- 4LNK · B. subtilis glutamine synthetase structures reveal large active site conformational… · the same entry in another collection · chain E against E, TM-score 1.00
- P12425 · AlphaFold monomer V2.0 prediction for glutamine synthetase (P12425) · a predicted model of the same protein · chain E 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 P12425
- Elsewhere: RCSB PDB 4LNK · PDBe 4LNK · UniProt P12425
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