Structure of PDB 2yyu Chain A Binding Site BS01

Receptor Information
>2yyu Chain A (length=225) Species: 235909 (Geobacillus kaustophilus HTA426) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
TPFIVALDFPSKQEVERFLRPFAGTPLFVKVGMELYYQEGPAIVAFLKEQ
GHAVFLDLKLHDIPNTVKQAMKGLARVGADLVNVHAAGGRRMMEAAIEGL
DAGTPSGRMRPRCIAVTQLTSTDERMLHEELWISRPLVETVAHYAALAKE
SGLDGVVCSANEAAFIKERCGASFLAVTPGIRFADRVVTPRKARALGSDY
IVIGRSLTRAADPLRTYARLQHEWN
Ligand information
Ligand IDC5P
InChIInChI=1S/C9H14N3O8P/c10-5-1-2-12(9(15)11-5)8-7(14)6(13)4(20-8)3-19-21(16,17)18/h1-2,4,6-8,13-14H,3H2,(H2,10,11,15)(H2,16,17,18)/t4-,6-,7-,8-/m1/s1
InChIKeyIERHLVCPSMICTF-XVFCMESISA-N
SMILES
SoftwareSMILES
CACTVS 3.341NC1=NC(=O)N(C=C1)[CH]2O[CH](CO[P](O)(O)=O)[CH](O)[CH]2O
OpenEye OEToolkits 1.5.0C1=CN(C(=O)N=C1N)C2C(C(C(O2)COP(=O)(O)O)O)O
CACTVS 3.341NC1=NC(=O)N(C=C1)[C@@H]2O[C@H](CO[P](O)(O)=O)[C@@H](O)[C@H]2O
OpenEye OEToolkits 1.5.0C1=CN(C(=O)N=C1N)[C@H]2[C@@H]([C@@H]([C@H](O2)COP(=O)(O)O)O)O
ACDLabs 10.04O=C1N=C(N)C=CN1C2OC(C(O)C2O)COP(=O)(O)O
FormulaC9 H14 N3 O8 P
NameCYTIDINE-5'-MONOPHOSPHATE
ChEMBLCHEMBL307679
DrugBankDB03403
ZINCZINC000003861744
PDB chain2yyu Chain A Residue 1301 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB2yyu Crystal structure of uncharacterized conserved protein from Geobacillus kaustophilus
Resolution2.2 Å
Binding residue
(original residue number in PDB)		D12 K34 T124 R186 G215 R216
Binding residue
(residue number reindexed from 1)		D8 K30 T120 R182 G204 R205
Annotation score3
Enzymatic activity
Catalytic site (original residue number in PDB) K34 D61 K63 D66 T124 R216
Catalytic site (residue number reindexed from 1) K30 D57 K59 D62 T120 R205
Enzyme Commision number 4.1.1.23: orotidine-5'-phosphate decarboxylase.
Gene Ontology
Molecular Function
GO:0004590 orotidine-5'-phosphate decarboxylase activity
GO:0016831 carboxy-lyase activity
Biological Process
GO:0006207 'de novo' pyrimidine nucleobase biosynthetic process
GO:0006221 pyrimidine nucleotide biosynthetic process
GO:0044205 'de novo' UMP biosynthetic process
Cellular Component
GO:0005829 cytosol

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:2yyu, PDBe:2yyu, PDBj:2yyu
PDBsum2yyu
PubMed
UniProtQ5L0U0|PYRF_GEOKA Orotidine 5'-phosphate decarboxylase (Gene Name=pyrF)

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