MolNFT v1 · #34041 · protein
Crystal structure of the maize glutamine synthetase complexed with amppnp and methionine sulfoximine
2D3B: “Crystal structure of the maize glutamine synthetase complexed with amppnp and methionine sulfoximine”. X-ray diffraction, 3 ligands (ANP, MSL, MN), 20 pockets (best druggability 0.75). MolNFT v1 #34041 on GenesisL1: 3D structure…
- PDB
- 2D3B
- 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
- ANP, MSL, 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
- ANP · Phosphoaminophosphonic acid-adenylate ester · ligand · 10 copies · chains A, B, C, E, D, F, G, H, J, I
- MSL · (2S)-2-amino-4-(methylsulfonimidoyl)butanoic acid · ligand · 10 copies · chains A, B, C, E, D, G, H, F, I, J
- 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 | 543 | 0.75 | 0.83 | 66 | MSL, MN, ANP |
| 2 | 503 | 0.75 | 0.83 | 62 | MSL, MN, ANP |
| 3 | 519 | 0.75 | 0.83 | 68 | MSL, MN, ANP |
| 4 | 564 | 0.74 | 0.82 | 67 | MN, MSL, ANP |
| 5 | 495 | 0.74 | 0.83 | 65 | MSL, MN, ANP |
Interfaces
20 interfaces between chains.
- I–J · 2032 Ų buried · 40 hydrogen bonds · protein-protein
- A–D · 2026 Ų buried · 38 hydrogen bonds · protein-protein
- B–C · 2026 Ų buried · 39 hydrogen bonds · protein-protein
- F–I · 2021 Ų buried · 39 hydrogen bonds · protein-protein
- C–E · 2020 Ų buried · 40 hydrogen bonds · protein-protein
Compared structures
- 2D3B · Crystal Structure of the Maize Glutamine Synthetase complexed with AMPPNP and Methionine… · 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 B 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 2D3B · PDBe 2D3B · UniProt P38561
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