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Structures of saicar synthetase (purc) from streptococcus pneumoniae with ADP, MG2+, air and L-asp
Analyse Structures of saicar synthetase (purc) from streptococcus pneumoniae with ADP… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4NYE
- Type
- protein
- Length
- 468 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
- Q07296
- Ligands
- ADP, MG, CL
- Pockets
- 3 · best druggability 0.78
Structure
x-ray diffraction · 2 distinct chains · 31% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Phosphoribosylaminoimidazole-succinocarboxamide synthase (EC 6.3.2.6) | protein | 235 | 31% helix, 30% strand | Q07296 |
| B | Phosphoribosylaminoimidazole-succinocarboxamide synthase (EC 6.3.2.6) | protein | 233 | 31% helix, 31% strand | Q07296 |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 2 copies · chains A, B
- CL · Chloride ion · ion · chains A, B
- ACT · Acetate ion · 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 | 609 | 0.78 | 0.84 | 51 | MG, ADP, ACT |
| 2 | 665 | 0.77 | 0.83 | 55 | MG, ADP, ACT |
| 3 | 97 | 0.50 | 0.82 | 21 | empty |
Interfaces
1 interface between chains.
- A–B · 903 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 4NYE · Structures of SAICAR Synthetase (PurC) from Streptococcus pneumoniae with ADP, Mg2+, AIR… · the same entry in another collection · chain A against A, TM-score 1.00
- Q07296 · 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 Q07296
- Elsewhere: RCSB PDB 4NYE · PDBe 4NYE · UniProt Q07296
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