Research workbench
Crystal structure of adenylosuccinate synthetase, pura, from thermus thermophilus
Analyse Crystal structure of adenylosuccinate synthetase, pura, from thermus… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6JRQ
- Type
- protein
- Length
- 1,628 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Adenylosuccinate synthetase
- EC
- 6.3.4.4
- UniProt
- Q5SLS1
- Ligands
- IMP
- Pockets
- 20 · best druggability 0.83
Structure
x-ray diffraction · 1 distinct chain · 37% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Adenylosuccinate synthetase (EC 6.3.4.4) | protein | 407 | 37% helix, 22% strand | Q5SLS1 |
Ligands and binding sites
- IMP · Inosinic acid · ligand · 4 copies · chains A, B, C, D
- EDO · 1,2-ethanediol · additive · 10 copies · chains A, D, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 913 | 0.83 | 0.85 | 120 | IMP, EDO |
| 2 | 134 | 0.81 | 0.99 | 26 | empty |
| 3 | 127 | 0.81 | 0.99 | 27 | empty |
| 4 | 482 | 0.79 | 0.87 | 70 | IMP |
| 5 | 710 | 0.76 | 0.82 | 81 | IMP |
Interfaces
4 interfaces between chains.
- C–D · 2791 Ų buried · 41 hydrogen bonds · protein-protein
- A–B · 2769 Ų buried · 40 hydrogen bonds · protein-protein
- A–D · 474 Ų buried · 5 hydrogen bonds · protein-protein
- B–C · 470 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 6JRQ · Crystal structure of adenylosuccinate synthetase, PurA, from Thermus thermophilus · the same entry in another collection · chain A against A, TM-score 1.00
- Q5SLS1 · AlphaFold monomer V2.0 prediction for adenylosuccinate synthetase (Q5SLS1) · 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 Q5SLS1
- Elsewhere: RCSB PDB 6JRQ · PDBe 6JRQ · UniProt Q5SLS1
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