Research workbench
Crystal structure of S. aureus glutamine synthetase in Met-Sox-P/ADP transition state complex
Analyse Crystal structure of S. aureus glutamine synthetase in Met-Sox-P/ADP transition… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7TDV
- Type
- protein
- Length
- 2,654 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.92
- Source
- Staphylococcus aureus
- Molecule
- Glutamine synthetase
- EC
- 6.3.1.2
- UniProt
- E3VXC2
- Ligands
- ADP, P3S, MG, SO4
- Pockets
- 20 · best druggability 0.81
Structure
x-ray diffraction · resolution 2.92 · 2 distinct chains · 38% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D, E, H | Glutamine synthetase (EC 6.3.1.2) | protein | 442 | 39% helix, 21% strand | E3VXC2 |
| C, B | Glutamine synthetase (EC 6.3.1.2) | protein | 443 | 38% helix, 21% strand | E3VXC2 |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · 6 copies · chains A, C, D, E, B, H
- P3S · L-methionine-S-sulfoximine phosphate · ligand · 6 copies · chains A, E, C, D, H, B
- MG · Magnesium ion · metal · 21 copies · chains A, C, D, E, B, H
- SO4 · Sulfate ion · ion · chains H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 16 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 432 | 0.81 | 0.89 | 57 | ADP, P3S, MG |
| 2 | 404 | 0.81 | 0.90 | 52 | ADP, P3S, MG |
| 3 | 403 | 0.81 | 0.89 | 55 | ADP, P3S, MG |
| 4 | 410 | 0.79 | 0.88 | 55 | ADP, P3S, MG |
| 5 | 322 | 0.78 | 0.89 | 43 | ADP, MG |
Interfaces
6 interfaces between chains.
- D–E · 1616 Ų buried · 27 hydrogen bonds · protein-protein
- D–H · 1595 Ų buried · 33 hydrogen bonds · protein-protein
- C–B · 1595 Ų buried · 31 hydrogen bonds · protein-protein
- A–C · 1582 Ų buried · 28 hydrogen bonds · protein-protein
- A–E · 1552 Ų buried · 30 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 covalent (covalent ligand).
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 E3VXC2
- Elsewhere: RCSB PDB 7TDV · PDBe 7TDV · UniProt E3VXC2
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