Structure of PDB 5wxk Chain A Binding Site BS01

Receptor Information
>5wxk Chain A (length=375) Species: 909420 (Neisseria meningitidis H44/76) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
PPFVCWIFCKVIDNFGDIGVSWRLARVLHRELGWQVHLWTDDVSALRALC
PDLPDVPCVHQDIHVRTWHSDAADIDTAPVPDVVIETFACDLPENVLHII
RRHKPLWLNWEYLSAEESNERLHLMPSPQEGVQKYFWFMGFSEKSGGLIR
ERDYCEAVRFDTEALRERLMLPEKNASEWLLFGYRSDVWAKWLEMWRQAG
SPMTLLLAGTQIIDSLKQSGVIPQDALQNDGDVFQTASVRLVKIPFVPQQ
DFDQLLHLADCAVIRGEDSFVRAQLAGKPFFWHIYPQDENVHLDKLHAFW
DKAHGFYTPETVSAHRRLSDDLNGGEALSATQRLECWQTLQQHQNGWRQG
AEDWSRYLFGQPSAPEKLAAFVSKH
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 chain5wxk Chain A Residue 401 [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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PDB5wxk Structural basis of protein arginine rhamnosylation by glycosyltransferase EarP
Resolution1.801 Å
Binding residue
(original residue number in PDB)		N17 F18 G19 L52 F185 Y187 F249 V250 Q252 F255 R268 E270 D271 S272
Binding residue
(residue number reindexed from 1)		N14 F15 G16 L49 F182 Y184 F246 V247 Q249 F252 R265 E267 D268 S269
Annotation score4
Enzymatic activity
Enzyme Commision number 2.4.1.-
Gene Ontology
Molecular Function
GO:0016757 glycosyltransferase activity
GO:0106361 protein-arginine rhamnosyltransferase activity

View graph for
Molecular Function
External links
PDB RCSB:5wxk, PDBe:5wxk, PDBj:5wxk
PDBsum5wxk
PubMed29440735
UniProtE6MVV9|EARP_NEIMH Protein-arginine rhamnosyltransferase (Gene Name=earP)

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