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Saicar synthetase (type-2) in complex with UMP/UDP

Analyse Saicar synthetase (type-2) in complex with UMP/UDP in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB
4O7R
Type
protein
Length
228 residues
Chains
1
Method
x-ray diffraction
Collection
MolNFT v1 / PDB
Contract
0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner
0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule
Phosphoribosylaminoimidazole-succinocarboxamide synthase
EC
6.3.2.6
UniProt
O57978
Ligands
U5P, UDP, PO4
Pockets
1 · best druggability 0.68

Structure

x-ray diffraction · 1 distinct chain · 31% helix, 32% strand (DSSP).

ChainMoleculeTypeResiduesSecondary structureUniProt
APhosphoribosylaminoimidazole-succinocarboxamide synthase (EC 6.3.2.6)protein22831% helix, 32% strandO57978

Ligands and binding sites

  • U5P · Uridine-5'-monophosphate · ligand · chains A
  • UDP · Uridine-5'-diphosphate · ligand · chains A
  • PO4 · Phosphate ion · ion · 2 copies · chains A
  • ACT · Acetate ion · additive · chains A

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.

PocketVolume (ų)DruggabilityBuriednessLining residuesInside
15640.680.7844U5P, PO4

Compared structures

  • 4O7R · SAICAR synthetase (Type-2) in complex with UMP/UDP · 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 A against A, TM-score 0.99

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