Structure of PDB 6dus Chain B Binding Site BS01

Receptor Information

>6dus Chain B (length=305) Species: 216597 (Salmonella enterica subsp. enterica serovar Typhimurium str. SL1344)

GSANFAGVEYPLLPLDQHTPLLFQWFERNPSRFGENQIPIINTQQNPYLN
NIINAAIIEKERTIGVLVDGNFSAGQKKALAKLEKQYENIKVIYNSDLDY
SMYDKKLSDIYLENIAKIEAQPADEYLLGEIKKSLNEVLKNNPEESLVSS
HDKRLGHVRFDFYRNLFLLKGSNAFLEAGKHGCHHLQPGGGCIYLDADML
LTGKLGTLYLPDGIAVHVSRKGNSMSLQNGIIAVNRSEHPALKKGLEIMH
SKPYGDPYIDGVCGGLRHYFNCSIRHNYEEFCNFIEFKHEHIFMDTSSLT
ISSWR

Ligand information

• Ligand ID: UDP
• InChI: InChI=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
• InChIKey: XCCTYIAWTASOJW-XVFCMESISA-N
• SMILES:
  OpenEye OEToolkits 1.7.0: C1=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 3.370: O[CH]1[CH](O)[CH](O[CH]1CO[P](O)(=O)O[P](O)(O)=O)N2C=CC(=O)NC2=O
  CACTVS 3.370: O[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 1.7.0: C1=CN(C(=O)NC1=O)C2C(C(C(O2)COP(=O)(O)OP(=O)(O)O)O)O
  ACDLabs 12.01: O=P(O)(O)OP(=O)(O)OCC2OC(N1C(=O)NC(=O)C=C1)C(O)C2O
• Formula: C9 H14 N2 O12 P2
• Name: URIDINE-5'-DIPHOSPHATE
• ChEMBL: CHEMBL130266
• DrugBank: DB03435
• ZINC: ZINC000004490939
• PDB chain: 6dus Chain B Residue 501

Receptor-Ligand Complex Structure

Structure summary

• PDB: 6dus Salmonella Effectors SseK1 and SseK3 Target Death Domain Proteins in the TNF and TRAIL Signaling Pathways.
• Resolution: 2.6 Å
• Binding residue (original residue number in PDB): Q51 W52 F53 Y75 F190 D226 D228 S327 S332 S333 W334 R335
• Binding residue (residue number reindexed from 1): Q24 W25 F26 Y48 F160 D196 D198 S297 S302 S303 W304 R305
• Annotation score: 4

Gene Ontology

Molecular Function

• GO:0000166 nucleotide binding
• GO:0016740 transferase activity
• GO:0046872 metal ion binding

External links

• PDB: RCSB:6dus, PDBe:6dus, PDBj:6dus
• PDBsum: 6dus
• PubMed: 30902834
• UniProt: A0A0H3NMP8