MolNFT v1 · #99636 · protein
The crystal structure of an adenylosuccinate synthetase from bacillus anthracis str. ames ancestor in complex with AMP.
4M9D: “The crystal structure of an adenylosuccinate synthetase from bacillus anthracis str. ames ancestor in complex…”. X-ray diffraction, 2 ligands (AMP, PO4), 6 pockets (best druggability 0.85). MolNFT v1 #99636 on GenesisL1: 3D…
- 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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