Research workbench
Saicar synthetase complexed with cair-MG2+ and ADP
Analyse Saicar synthetase complexed with cair-MG2+ and ADP in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2GQS
- Type
- protein
- Length
- 474 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Phosphoribosylaminoimidazole-succinocarboxamide synthase
- EC
- 6.3.2.6
- UniProt
- P0A7D7
- Ligands
- ADP, C2R, MG
- Pockets
- 3 · best druggability 0.82
Structure
x-ray diffraction · 1 distinct chain · 34% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Phosphoribosylaminoimidazole-succinocarboxamide synthase (EC 6.3.2.6) | protein | 237 | 34% helix, 33% strand | P0A7D7 |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · 2 copies · chains A, B
- C2R · 5-amino-1-(5-O-phosphono-beta-D-ribofuranosyl)-1H-imidazole-4-carboxylic acid · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 6 copies · chains A, B
- FMT · Formic acid · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1073 | 0.82 | 0.83 | 107 | MG, ADP, C2R, FMT |
| 2 | 187 | 0.52 | 0.78 | 36 | empty |
| 3 | 62 | 0.31 | 0.75 | 13 | empty |
Interfaces
1 interface between chains.
- A–B · 980 Ų buried · 18 hydrogen bonds · protein-protein
Compared structures
- 2GQS · SAICAR Synthetase Complexed with CAIR-Mg2+ and ADP · the same entry in another collection · chain A against A, TM-score 1.00
- P0A7D7 · AlphaFold monomer V2.0 prediction for phosphoribosylaminoimidazole- succinocarboxamide… · 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 P0A7D7
- Elsewhere: RCSB PDB 2GQS · PDBe 2GQS · UniProt P0A7D7
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