Structure of PDB 4dmw Chain A Binding Site BS02

Receptor Information
>4dmw Chain A (length=535) Species: 1496 (Clostridioides difficile) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
SLISKEELIKLAYSIRPRENEYKTILTNLDEYNKLTTNNNENKYLQLKKL
NESIDVFMNKYKTSSRNRALSNLKKDILKEVILIKNSNTSPVEKNLHFVW
IGGEVSDIALEYIKQWADINAEYNIKLWYDSEAFLVNTLKKAIVESSTTE
ALQLLEEEIQNPQFDNMKFYKKRMEFIYDRQKRFINYYKSQINKVPTIDD
IIKSHLVSEYNRDETVLESYRTNSLRKINSNHGIDIRANSLFTEQELLNI
YSQELLNRGNLAAASDIVRLLALKNFGGVYLDVDMLPGIHSDLFKTISRP
SSIGLDRWEMIKLEAIMKYKKYINNYTSENFDKLDQQLKDNFKLIIESKS
EKSEIFSKLENLNVSDLEIKIAFALGSVINQALISKQGSYLTNLVIEQVK
NRYQFLNQHLNPAIESDNNFTDTTKIFHDSLFNSATAENSMFLTKIAPYL
QVGFMPEARSTISLSGPGAYASAYYDFINLQENTIEKTLKASDLIEFKFP
ENNLSQLTEQEINSLWSFDQASAKYQFEKYVRDYT
Ligand information
Ligand IDUDP
InChIInChI=1S/C9H14N2O12P2/c12-5-1-2-11(9(15)10-5)8-7(14)6(13)4(22-8)3-21-25(19,20)23-24(16,17)18/h1-2,4,6-8,13-14H,3H2,(H,19,20)(H,10,12,15)(H2,16,17,18)/t4-,6-,7-,8-/m1/s1
InChIKeyXCCTYIAWTASOJW-XVFCMESISA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.0C1=CN(C(=O)NC1=O)[C@H]2[C@@H]([C@@H]([C@H](O2)CO[P@@](=O)(O)OP(=O)(O)O)O)O
CACTVS 3.370O[CH]1[CH](O)[CH](O[CH]1CO[P](O)(=O)O[P](O)(O)=O)N2C=CC(=O)NC2=O
CACTVS 3.370O[C@H]1[C@@H](O)[C@@H](O[C@@H]1CO[P](O)(=O)O[P](O)(O)=O)N2C=CC(=O)NC2=O
OpenEye OEToolkits 1.7.0C1=CN(C(=O)NC1=O)C2C(C(C(O2)COP(=O)(O)OP(=O)(O)O)O)O
ACDLabs 12.01O=P(O)(O)OP(=O)(O)OCC2OC(N1C(=O)NC(=O)C=C1)C(O)C2O
FormulaC9 H14 N2 O12 P2
NameURIDINE-5'-DIPHOSPHATE
ChEMBLCHEMBL130266
DrugBankDB03435
ZINCZINC000004490939
PDB chain4dmw Chain A Residue 602 [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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PDB4dmw The structure of Clostridium difficile toxin A glucosyltransferase domain bound to Mn2+ and UDP provides insights into glucosyltransferase activity and product release.
Resolution2.5 Å
Binding residue
(original residue number in PDB)		V100 W101 I102 L264 S268 D285 S517
Binding residue
(residue number reindexed from 1)		V99 W100 I101 L261 S265 D282 S514
Annotation score3
Binding affinityPDBbind-CN: -logKd/Ki=4.94,Kd=11.4uM
Enzymatic activity
Enzyme Commision number 2.4.1.-
3.4.22.-
Gene Ontology
Molecular Function
GO:0016757 glycosyltransferase activity

View graph for
Molecular Function
External links
PDB RCSB:4dmw, PDBe:4dmw, PDBj:4dmw
PDBsum4dmw
PubMed22747490
UniProtP16154|TCDA_CLODI Toxin A (Gene Name=tcdA)

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