Structure of PDB 1km3 Chain A

Receptor sequence
>1km3A (length=212) Species: 145262 (Methanothermobacter thermautotrophicus) [Search protein sequence]
VMNRLILAMDLMNRDDALRVTGEVREYIDTVAIGYPLVLSEGMDIIAEFR
KRFGCRIIADFKVADIPETNEKICRATFKAGADAIIVHGFPGADSVRACL
NVAEEMGREVFLLTEMSHPGAEMFIQGAADEIARMGVDLGVKNYVGPSTR
PERLSRLREIIGQDSFLISPGVGAQGGDPGETLRFADAIIVGRSIYLADN
PAAAAAGIIESI
3D structure
PDB1km3 Mapping the active site-ligand interactions of orotidine 5'-monophosphate decarboxylase by crystallography.
ChainA
Resolution1.5 Å
3D
structure
Catalytic site residues are labeled in the structure
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Enzymatic activity
Catalytic site (original residue number in PDB) A42 D70 K72 D75
Catalytic site (residue number reindexed from 1) A32 D60 K62 D65
Enzyme Commision number 4.1.1.23: orotidine-5'-phosphate decarboxylase.
Interaction with ligand
Site
#		 Ligand Ligand
chain		 Binding residues on receptor
(original residue number in PDB)		 Binding residues on receptor
(residue number reindexed from 1)		 Binding affinity
BS01 UP6 A D20 K72 M126 S127 P180 Q185 G202 R203 D10 K62 M116 S117 P170 Q175 G192 R193 PDBbind-CN: -logKd/Ki=4.91,Ki=12.4uM
BindingDB: Ki=12400nM
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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Cellular Component
External links
PDB RCSB:1km3, PDBe:1km3, PDBj:1km3
PDBsum1km3
PubMed11900543
UniProtO26232|PYRF_METTH Orotidine 5'-phosphate decarboxylase (Gene Name=pyrF)

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