Structure of PDB 3lhz Chain A Binding Site BS01

Receptor Information
>3lhz Chain A (length=218) Species: 187420 (Methanothermobacter thermautotrophicus str. Delta H) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
VMDVMNRLILAMDLMNRDDALRVTGEVREYIDTVKIGYPLVLSEGMDIIA
EFRKRFGCRIIADFKVADIPETNEKICRATFKAGADAIIVHGFPGADSVR
ACLNVAEEMGREVFLLTEMSHPGAEMFIQGAADEIARMGVDLGVKNYVGP
STRPERLSRLREIIGQDSFLISPGVGAQGGDPGETLRFADAIIAGRSIYL
ADNPAAAAAGIIESIKDL
Ligand information
Ligand IDBMQ
InChIInChI=1S/C9H13N2O10P/c12-4-1-5(13)11(9(16)10-4)8-7(15)6(14)3(21-8)2-20-22(17,18)19/h3,6-8,14-15H,1-2H2,(H,10,12,16)(H2,17,18,19)/t3-,6-,7-,8-/m1/s1
InChIKeyAODYJUNLDJOADV-YXZULKJRSA-N
SMILES
SoftwareSMILES
CACTVS 3.370O[C@H]1[C@@H](O)[C@@H](O[C@@H]1CO[P](O)(O)=O)N2C(=O)CC(=O)NC2=O
CACTVS 3.370O[CH]1[CH](O)[CH](O[CH]1CO[P](O)(O)=O)N2C(=O)CC(=O)NC2=O
ACDLabs 12.01O=P(O)(O)OCC2OC(N1C(=O)NC(=O)CC1=O)C(O)C2O
OpenEye OEToolkits 1.7.2C1C(=O)NC(=O)N(C1=O)C2C(C(C(O2)COP(=O)(O)O)O)O
OpenEye OEToolkits 1.7.2C1C(=O)NC(=O)N(C1=O)[C@H]2[C@@H]([C@@H]([C@H](O2)COP(=O)(O)O)O)O
FormulaC9 H13 N2 O10 P
Name1-(5'-PHOSPHO-BETA-D-RIBOFURANOSYL)BARBITURIC ACID
ChEMBLCHEMBL1231399
DrugBankDB03668
ZINCZINC000001559604
PDB chain3lhz Chain A Residue 229 [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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PDB3lhz Conformational changes in orotidine 5'-monophosphate decarboxylase: "remote" residues that stabilize the active conformation.
Resolution1.4 Å
Binding residue
(original residue number in PDB)		D20 K72 M126 S127 P180 Q185 G202 R203
Binding residue
(residue number reindexed from 1)		D13 K65 M119 S120 P173 Q178 G195 R196
Annotation score2
Enzymatic activity
Catalytic site (original residue number in PDB) K42 D70 K72 D75
Catalytic site (residue number reindexed from 1) K35 D63 K65 D68
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:3lhz, PDBe:3lhz, PDBj:3lhz
PDBsum3lhz
PubMed20369850
UniProtO26232|PYRF_METTH Orotidine 5'-phosphate decarboxylase (Gene Name=pyrF)

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