Research workbench
Saicar synthetase (type-1) in complex with ADP and AMP
Analyse Saicar synthetase (type-1) in complex with ADP and AMP in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4O81
- Type
- protein
- Length
- 452 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
- O57978
- Ligands
- AMP, ADP, CD
- Pockets
- 4 · best druggability 0.73
Structure
x-ray diffraction · 2 distinct chains · 31% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Phosphoribosylaminoimidazole-succinocarboxamide synthase (EC 6.3.2.6) | protein | 227 | 30% helix, 33% strand | O57978 |
| B | Phosphoribosylaminoimidazole-succinocarboxamide synthase (EC 6.3.2.6) | protein | 225 | 31% helix, 32% strand | O57978 |
Ligands and binding sites
- AMP · Adenosine monophosphate · ligand · 3 copies · chains A, B
- ADP · Adenosine-5'-diphosphate · ligand · chains B
- CD · Cadmium ion · metal · 17 copies · chains A, B
- BU1 · 1,4-butanediol · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 733 | 0.73 | 0.79 | 64 | CD |
| 2 | 509 | 0.64 | 0.76 | 47 | CD, AMP |
| 3 | 441 | 0.61 | 0.76 | 31 | CD, AMP |
| 4 | 50 | 0.30 | 0.76 | 16 | ADP |
Interfaces
1 interface between chains.
- A–B · 314 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 modified (engineered).
Compared structures
- 4O81 · SAICAR synthetase (Type-1) in complex with ADP AND AMP · the same entry in another collection · chain A against A, TM-score 1.00
- O57978 · AlphaFold monomer V2.0 prediction for phosphoribosylaminoimidazole- succinocarboxamide… · a predicted model of the same protein · chain B 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 O57978
- Elsewhere: RCSB PDB 4O81 · PDBe 4O81 · UniProt O57978
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