Research workbench
Entrapment of 6-thiophosphoryl-imp in the active site of crystalline adenylosuccinate synthetase from escherichia COLI, data collected at 298K
Analyse Entrapment of 6-thiophosphoryl-imp in the active site of crystalline… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1KSZ
- Type
- protein
- Length
- 431 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Adenylosuccinate synthetase
- EC
- 6.3.4.4
- UniProt
- P0A7D4
- Ligands
- GDP, HDA, PGS, MG
- Pockets
- 4 · best druggability 0.76
Structure
x-ray diffraction · 1 distinct chain · 38% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Adenylosuccinate synthetase (EC 6.3.4.4) | protein | 431 | 38% helix, 21% strand | P0A7D4 |
Ligands and binding sites
- GDP · Guanosine-5'-diphosphate · ligand · chains A
- HDA · Hadacidin · ligand · chains A
- PGS · 2-deazo-6-thiophosphate guanosine-5'-monophosphate · ligand · chains A
- MG · Magnesium ion · metal · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 297 | 0.76 | 0.88 | 47 | HDA, PGS |
| 2 | 256 | 0.65 | 0.83 | 28 | GDP |
| 3 | 75 | 0.38 | 0.78 | 16 | empty |
| 4 | 50 | 0.29 | 0.76 | 15 | empty |
Compared structures
- 1KSZ · Entrapment of 6-thiophosphoryl-imp in the active site of crystalline adenylosuccinate… · the same entry in another collection · chain A against A, TM-score 1.00
- P0A7D4 · AlphaFold monomer V2.0 prediction for adenylosuccinate synthetase (P0A7D4) · 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 P0A7D4
- Elsewhere: RCSB PDB 1KSZ · PDBe 1KSZ · UniProt P0A7D4
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