MolNFT v1 · #13789 · protein
Crystal structure of the recombinant mouse-muscle adenylosuccinate synthetase complexed with 6-phosphoryl-imp, GDP and mg
1LNY: “Crystal structure of the recombinant mouse-muscle adenylosuccinate synthetase complexed with…”. X-ray diffraction, 3 ligands (IMO, GDP, MG), 11 pockets (best druggability 0.83). MolNFT v1 #13789 on GenesisL1: 3D structure, binding…
- PDB
- 1LNY
- Type
- protein
- Length
- 861 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Adenylosuccinate synthetase
- EC
- 6.3.4.4
- UniProt
- P28650
- Ligands
- IMO, GDP, MG
- Pockets
- 11 · best druggability 0.83
Structure
x-ray diffraction · 2 distinct chains · 38% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Adenylosuccinate synthetase (EC 6.3.4.4) | protein | 430 | 38% helix, 22% strand | P28650 |
| B | Adenylosuccinate synthetase (EC 6.3.4.4) | protein | 431 | 39% helix, 22% strand | P28650 |
Ligands and binding sites
- IMO · 6-O-phosphoryl inosine monophosphate · ligand · 2 copies · chains A, B
- GDP · Guanosine-5'-diphosphate · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 149 | 0.83 | 0.99 | 21 | empty |
| 2 | 482 | 0.81 | 0.88 | 57 | empty |
| 3 | 604 | 0.79 | 0.85 | 68 | GDP, IMO |
| 4 | 262 | 0.77 | 0.90 | 47 | IMO |
| 5 | 223 | 0.69 | 0.86 | 31 | GDP |
Interfaces
1 interface between chains.
- A–B · 2911 Ų buried · 37 hydrogen bonds · protein-protein
Compared structures
- 1LNY · Crystal structure of the recombinant mouse-muscle adenylosuccinate synthetase complexed… · the same entry in another collection · chain A against A, TM-score 1.00
- P28650 · AlphaFold monomer V2.0 prediction for adenylosuccinate synthetase isozyme 1 (P28650) · a predicted model of the same protein · chain A against A, TM-score 0.99
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 P28650
- Elsewhere: RCSB PDB 1LNY · PDBe 1LNY · UniProt P28650
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