Research workbench
Crystal structure of the maize glutamine synthetase complexed with ADP and phosphinothricin phosphate
Analyse Crystal structure of the maize glutamine synthetase complexed with ADP and… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2D3C
- Type
- protein
- Length
- 3,530 residues
- Chains
- 10
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glutamine synthetase
- EC
- 6.3.1.2
- UniProt
- P38561
- Ligands
- P3P, ADP, MN
- Pockets
- 20 · best druggability 0.75
Structure
x-ray diffraction · 1 distinct chain · 30% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F, G, H, I, J | Glutamine synthetase (EC 6.3.1.2) | protein | 353 | 30% helix, 25% strand | P38561 |
Ligands and binding sites
- P3P · (2S)-2-amino-4-[methyl(phosphonooxy)phosphoryl]butanoic acid · ligand · 10 copies · chains A, B, C, E, D, F, G, H, J, I
- ADP · Adenosine-5'-diphosphate · ligand · 10 copies · chains A, B, C, E, D, F, G, H, J, I
- MN · Manganese (II) ion · metal · 30 copies · chains A, B, C, D, E, F, G, H, I, J
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.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 499 | 0.75 | 0.84 | 64 | MN, P3P, ADP |
| 2 | 525 | 0.75 | 0.83 | 64 | MN, P3P, ADP |
| 3 | 565 | 0.75 | 0.83 | 65 | MN, P3P, ADP |
| 4 | 546 | 0.75 | 0.83 | 62 | MN, P3P, ADP |
| 5 | 550 | 0.75 | 0.83 | 69 | MN, P3P, ADP |
Interfaces
20 interfaces between chains.
- C–E · 2021 Ų buried · 38 hydrogen bonds · protein-protein
- I–J · 2013 Ų buried · 38 hydrogen bonds · protein-protein
- F–G · 2013 Ų buried · 39 hydrogen bonds · protein-protein
- A–D · 2009 Ų buried · 39 hydrogen bonds · protein-protein
- B–C · 2008 Ų buried · 40 hydrogen bonds · protein-protein
Compared structures
- 2D3C · Crystal Structure of the Maize Glutamine Synthetase complexed with ADP and… · the same entry in another collection · chain J against J, TM-score 1.00
- P38561 · AlphaFold monomer V2.0 prediction for glutamine synthetase root isozyme 3 (P38561) · a predicted model of the same protein · chain A against A, 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 P38561
- Elsewhere: RCSB PDB 2D3C · PDBe 2D3C · UniProt P38561
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