Structure of PDB 5wcn Chain A Binding Site BS01

Receptor Information

>5wcn Chain A (length=382) Species: 75985 (Mannheimia haemolytica)

MFLKFHLAEDYRKTTNLFFISQMGQLEQYQGLIEKLKLKNNVLIVLYTAA
NQLMPKNIAERCNKELFNSIRFLCLPKSPMRLNIKNYIMMLNSYKLLLKR
IKPKELYISSFERHYSLLGTLAKNMGFKVNLVEEGTGTYKYSSMQEACKK
LDDSMNYQEKKVYKKISKSFIYKNIRSSLKPFDSFDHIYVAFPEKVKNVF
KCNKISFFSIYESRLENEHVSEFIRNNKCSKKNIIFCAQRYPIPEREYIS
TILDILYKYAKEYKTKVFIKLHPKERIETIDVYKEISKDKQGLIIMENIS
FPAEDFISQLKPRKVLSIASTSLVYTTLISKDIKAISIYPLFRKEVLKKI
EYKEEYFKDIESHYSLLSKFDGIRILNNTNEI

Ligand information

• Ligand ID: CDP
• InChI: InChI=1S/C9H15N3O11P2/c10-5-1-2-12(9(15)11-5)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)(H2,10,11,15)(H2,16,17,18)/t4-,6-,7-,8-/m1/s1
• InChIKey: ZWIADYZPOWUWEW-XVFCMESISA-N
• SMILES:
  OpenEye OEToolkits 1.5.0: C1=CN(C(=O)N=C1N)C2C(C(C(O2)COP(=O)(O)OP(=O)(O)O)O)O
  CACTVS 3.341: NC1=NC(=O)N(C=C1)[C@@H]2O[C@H](CO[P@](O)(=O)O[P](O)(O)=O)[C@@H](O)[C@H]2O
  ACDLabs 10.04: O=P(O)(O)OP(=O)(O)OCC2OC(N1C(=O)N=C(N)C=C1)C(O)C2O
  OpenEye OEToolkits 1.5.0: C1=CN(C(=O)N=C1N)[C@H]2[C@@H]([C@@H]([C@H](O2)CO[P@@](=O)(O)OP(=O)(O)O)O)O
  CACTVS 3.341: NC1=NC(=O)N(C=C1)[CH]2O[CH](CO[P](O)(=O)O[P](O)(O)=O)[CH](O)[CH]2O
• Formula: C9 H15 N3 O11 P2
• Name: CYTIDINE-5'-DIPHOSPHATE
• ChEMBL: CHEMBL425252
• DrugBank: DB04555
• ZINC: ZINC000008215624
• PDB chain: 5wcn Chain A Residue 502

Receptor-Ligand Complex Structure

Structure summary

• PDB: 5wcn X-ray crystallographic structure of a bacterial polysialyltransferase provides insight into the biosynthesis of capsular polysialic acid.
• Resolution: 3.0 Å
• Binding residue (original residue number in PDB): A257 K289 L290 A322 E323 S339
• Binding residue (residue number reindexed from 1): A238 K270 L271 A303 E304 S320
• Annotation score: 4

Gene Ontology

Molecular Function

• GO:0000166 nucleotide binding

External links

• PDB: RCSB:5wcn, PDBe:5wcn, PDBj:5wcn
• PDBsum: 5wcn
• PubMed: 28724897
• UniProt: G4RIN4