Structure of PDB 3ryk Chain B Binding Site BS01

Receptor Information
>3ryk Chain B (length=175) Species: 198094 (Bacillus anthracis str. Ames) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
AMKVIETNFTDAKLLEPRLFGDDRGFFTESYNKKVLETLGVTHSFVQDNV
SYSAEAGTIRGLHFQKNPKAQTKLIQVMQGAIYDVIVDLRKDSPTFKQWR
GYILSADNHRQLLVPKGFAHGFCTLVPHTIVMYKVDEYYSADHDSGVLWN
DKELAIPWPVTSPILSDKDRILPLL
Ligand information
Ligand IDTYD
InChIInChI=1S/C10H16N2O11P2/c1-5-3-12(10(15)11-9(5)14)8-2-6(13)7(22-8)4-21-25(19,20)23-24(16,17)18/h3,6-8,13H,2,4H2,1H3,(H,19,20)(H,11,14,15)(H2,16,17,18)/t6-,7+,8+/m0/s1
InChIKeyUJLXYODCHAELLY-XLPZGREQSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0CC1=CN(C(=O)NC1=O)[C@H]2C[C@@H]([C@H](O2)CO[P@](=O)(O)OP(=O)(O)O)O
OpenEye OEToolkits 1.5.0CC1=CN(C(=O)NC1=O)C2CC(C(O2)COP(=O)(O)OP(=O)(O)O)O
ACDLabs 10.04O=P(O)(O)OP(=O)(O)OCC2OC(N1C(=O)NC(=O)C(=C1)C)CC2O
CACTVS 3.341CC1=CN([CH]2C[CH](O)[CH](CO[P](O)(=O)O[P](O)(O)=O)O2)C(=O)NC1=O
CACTVS 3.341CC1=CN([C@H]2C[C@H](O)[C@@H](CO[P@@](O)(=O)O[P](O)(O)=O)O2)C(=O)NC1=O
FormulaC10 H16 N2 O11 P2
NameTHYMIDINE-5'-DIPHOSPHATE
ChEMBLCHEMBL259724
DrugBankDB03103
ZINCZINC000008215882
PDB chain3ryk Chain B Residue 182 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB3ryk Structure of the Bacillus anthracis dTDP-L-rhamnose-biosynthetic enzyme dTDP-4-dehydrorhamnose 3,5-epimerase (RfbC).
Resolution1.631 Å
Binding residue
(original residue number in PDB)		Q46 Y138 S165
Binding residue
(residue number reindexed from 1)		Q47 Y139 S166
Annotation score2
Enzymatic activity
Catalytic site (original residue number in PDB) H62 K72 Y132 D168
Catalytic site (residue number reindexed from 1) H63 K73 Y133 D169
Enzyme Commision number 5.1.3.13: dTDP-4-dehydrorhamnose 3,5-epimerase.
Gene Ontology
Molecular Function
GO:0008830 dTDP-4-dehydrorhamnose 3,5-epimerase activity
GO:0016853 isomerase activity
GO:0051213 dioxygenase activity
Biological Process
GO:0019305 dTDP-rhamnose biosynthetic process
GO:0045226 extracellular polysaccharide 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:3ryk, PDBe:3ryk, PDBj:3ryk
PDBsum3ryk
PubMed29199987
UniProtA0A6L7H6N0

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