Structure of PDB 6ypo Chain A Binding Site BS01

Receptor Information
>6ypo Chain A (length=312) Species: 3702 (Arabidopsis thaliana) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
PHMFELSDVIEGKQFDREMLSAIFDVAREMEKIEKSSSQSEILKGYLMAT
LFYEPSTRTRLSFESAMKRLGGEVLTTENAREFSSAAKGETLEDTIRTVE
GYSDIIVMRHFESGAARKAAATANIPVINAGDGPGEHPTQALLDVYTIQS
EIGKLDGISVALVGDLANGRTVRSLAYLLAKFKDVKIYFVSPEIVKMKDD
IKDYLTSSGVEWEESSDLMEVASKCDVVYQTRIQRERFGERLDLYEAARG
KFIVDKDLLGVMQKKAIIMHPLPRLDEITADVDADPRAAYFRQAKNGLFI
RMALLKLLLVGW
Ligand information
Ligand IDU5P
InChIInChI=1S/C9H13N2O9P/c12-5-1-2-11(9(15)10-5)8-7(14)6(13)4(20-8)3-19-21(16,17)18/h1-2,4,6-8,13-14H,3H2,(H,10,12,15)(H2,16,17,18)/t4-,6-,7-,8-/m1/s1
InChIKeyDJJCXFVJDGTHFX-XVFCMESISA-N
SMILES
SoftwareSMILES
ACDLabs 10.04O=C1NC(=O)N(C=C1)C2OC(C(O)C2O)COP(=O)(O)O
CACTVS 3.341O[CH]1[CH](O)[CH](O[CH]1CO[P](O)(O)=O)N2C=CC(=O)NC2=O
OpenEye OEToolkits 1.5.0C1=CN(C(=O)NC1=O)[C@H]2[C@@H]([C@@H]([C@H](O2)COP(=O)(O)O)O)O
OpenEye OEToolkits 1.5.0C1=CN(C(=O)NC1=O)C2C(C(C(O2)COP(=O)(O)O)O)O
CACTVS 3.341O[C@H]1[C@@H](O)[C@@H](O[C@@H]1CO[P](O)(O)=O)N2C=CC(=O)NC2=O
FormulaC9 H13 N2 O9 P
NameURIDINE-5'-MONOPHOSPHATE
ChEMBLCHEMBL214393
DrugBankDB03685
ZINCZINC000002123545
PDB chain6ypo Chain A Residue 401 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB6ypo Mechanisms of feedback inhibition and sequential firing of active sites in plant aspartate transcarbamoylase.
Resolution1.67 Å
Binding residue
(original residue number in PDB)		R136 T137 R187 H215 R248 T249 R310 H348 P349 L350
Binding residue
(residue number reindexed from 1)		R58 T59 R109 H137 R170 T171 R232 H270 P271 L272
Annotation score1
Enzymatic activity
Catalytic site (original residue number in PDB) R187 H215 Q218 T309 P349 G375
Catalytic site (residue number reindexed from 1) R109 H137 Q140 T231 P271 G297
Enzyme Commision number 2.1.3.2: aspartate carbamoyltransferase.
Gene Ontology
Molecular Function
GO:0004070 aspartate carbamoyltransferase activity
GO:0016597 amino acid binding
GO:0016743 carboxyl- or carbamoyltransferase activity
Biological Process
GO:0006207 'de novo' pyrimidine nucleobase biosynthetic process
GO:0006520 amino acid metabolic process

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Molecular Function
View graph for
Biological Process
External links
PDB RCSB:6ypo, PDBe:6ypo, PDBj:6ypo
PDBsum6ypo
PubMed33574254
UniProtP49077|PYRB_ARATH Aspartate carbamoyltransferase, chloroplastic (Gene Name=PYRB)

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