Structure of PDB 2ixi Chain B Binding Site BS02

Receptor Information
>2ixi Chain B (length=184) Species: 287 (Pseudomonas aeruginosa) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
SMSMKATRLAIPDVILFEPRVFGDDRGFFFESYNQRAFEEACGHPVSFVQ
DNHSRSARGVLRGLHYQIRQAQGKLVRATLGEVFDVAVDLRRGSPTFGQW
VGERLSAENKRQMWIPAGFAHGFVVLSEYAEFLYKTTDFWAPEHERCIVW
NDPELKIDWPLQDAPLLSEKDRQGKAFADADCFP
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 chain2ixi Chain B Residue 1182 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB2ixi Rmlc, a C3' and C5' Carbohydrate Epimerase, Appears to Operate Via an Intermediate with an Unusual Twist Boat Conformation.
Resolution1.8 Å
Binding residue
(original residue number in PDB)		W137 K167
Binding residue
(residue number reindexed from 1)		W140 K170
Annotation score2
Binding affinityMOAD: Ka=1320M^-1
Enzymatic activity
Catalytic site (original residue number in PDB) H62 K71 Y131 D168
Catalytic site (residue number reindexed from 1) H65 K74 Y134 D171
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
Biological Process
GO:0009103 lipopolysaccharide biosynthetic process
GO:0009244 lipopolysaccharide core region biosynthetic 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:2ixi, PDBe:2ixi, PDBj:2ixi
PDBsum2ixi
PubMed17046787
UniProtQ9HU21|RMLC_PSEAE dTDP-4-dehydrorhamnose 3,5-epimerase (Gene Name=rmlC)

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