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The crystal structure of an adenylosuccinate synthetase from bacillus anthracis str. ames ancestor in complex with AMP.
Analyse The crystal structure of an adenylosuccinate synthetase from bacillus anthracis… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4M9D
- Type
- protein
- Length
- 854 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Adenylosuccinate synthetase
- EC
- 6.3.4.4
- UniProt
- Q81JI9
- Ligands
- AMP, PO4
- Pockets
- 6 · best druggability 0.85
Structure
x-ray diffraction · 2 distinct chains · 39% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Adenylosuccinate synthetase (EC 6.3.4.4) | protein | 423 | 38% helix, 22% strand | Q81JI9 |
| B | Adenylosuccinate synthetase (EC 6.3.4.4) | protein | 431 | 39% helix, 22% strand | Q81JI9 |
Ligands and binding sites
- AMP · Adenosine monophosphate · ligand · 2 copies · chains A, B
- PO4 · Phosphate ion · ion · chains B
- EDO · 1,2-ethanediol · additive · 6 copies · chains A, B
- MLI · Malonate ion · additive · 3 copies · chains A, B
- FMT · Formic acid · additive · 3 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 208 | 0.85 | 0.99 | 29 | empty |
| 2 | 529 | 0.79 | 0.85 | 59 | empty |
| 3 | 755 | 0.78 | 0.82 | 76 | AMP, MLI, EDO |
| 4 | 709 | 0.76 | 0.82 | 69 | AMP, MLI, EDO, FMT, PO4 |
| 5 | 68 | 0.32 | 0.74 | 15 | FMT |
Interfaces
1 interface between chains.
- A–B · 2926 Ų buried · 36 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 modified (engineered).
Compared structures
- 4M9D · The Crystal structure of an adenylosuccinate synthetase from Bacillus anthracis str. Ames… · the same entry in another collection · chain A against A, TM-score 1.00
- Q81JI9 · AlphaFold monomer V2.0 prediction for adenylosuccinate synthetase (Q81JI9) · 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 Q81JI9
- Elsewhere: RCSB PDB 4M9D · PDBe 4M9D · UniProt Q81JI9
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