Structure of PDB 4yw2 Chain B Binding Site BS01

Receptor Information

>4yw2 Chain B (length=659) Species: 170187 (Streptococcus pneumoniae TIGR4)

ETPVLEKNNVTLTGGGENVTKELKDKFTSGDFTVVIKYNQSSEKGLQALF
GISNSKPGQQNSYVDVFLRDNGELGMEARDTSSNKNNLVSRPASVWGKYK
QEAVTNTVAVVADSVKKTYSLYANGTKVVEKKVDNFLNIKDIKGIDYYML
GGVKRAGKTAFGFNGTLENIKFFNSALDEETVKKMTTNAVTGHLIYTAND
TTGSNYFRIPVLYTFSNGRVFSSIDARYGGTHDFLNKINIATSYSDDNGK
TWTKPKLTLAFDDFAPVPLEWPREVGGRDLQISGGATYIDSVIVEKKNKQ
VLMFADVMPAGVSFREATRKDSGYKQIDGNYYLKLRKQGDTDYNYTIREN
GTVYDDRTNRPTEFSVDKNFGIKQNGNYLTVEQYSVSFENNKKTEYRNGT
KVHMNIFYKDALFKVVPTNYIAYISSNDHGESWSAPTLLPPIMGLNRNAP
YLGPGRGIIESSTGRILIPSYTGKESAFIYSDDNGASWKVKVVPLPSSWS
AEAQFVELSPGVIQAYMRTNNGKIAYLTSKDAGTTWSAPEYLKFVSNPSY
GTQLSIINYSQLIDGKKAVILSTPNSTNGRKHGQIWIGLINDDNTIDWRY
HHDVDYSNYGYSYSTLTELPNHEIGLMFEKFDSWSRNELHMKNVVPYITF
KIEDLKKNL

Ligand information

• Ligand ID: SIA
• InChI: InChI=1S/C11H19NO9/c1-4(14)12-7-5(15)2-11(20,10(18)19)21-9(7)8(17)6(16)3-13/h5-9,13,15-17,20H,2-3H2,1H3,(H,12,14)(H,18,19)/t5-,6+,7+,8+,9+,11+/m0/s1
• InChIKey: SQVRNKJHWKZAKO-YRMXFSIDSA-N
• SMILES:
  CACTVS 3.341: CC(=O)N[CH]1[CH](O)C[C](O)(O[CH]1[CH](O)[CH](O)CO)C(O)=O
  OpenEye OEToolkits 1.5.0: CC(=O)NC1C(CC(OC1C(C(CO)O)O)(C(=O)O)O)O
  OpenEye OEToolkits 1.5.0: CC(=O)N[C@@H]1[C@H](C[C@@](O[C@H]1[C@@H]([C@@H](CO)O)O)(C(=O)O)O)O
  ACDLabs 10.04: O=C(O)C1(O)OC(C(O)C(O)CO)C(NC(=O)C)C(O)C1
  CACTVS 3.341: CC(=O)N[C@@H]1[C@@H](O)C[C@@](O)(O[C@H]1[C@H](O)[C@H](O)CO)C(O)=O
• Formula: C11 H19 N O9
• Name: N-acetyl-alpha-neuraminic acid;
  N-acetylneuraminic acid;
  sialic acid;
  alpha-sialic acid;
  O-SIALIC ACID
• ChEMBL: CHEMBL1234621
• DrugBank: DB03721
• ZINC: ZINC000004081651
• PDB chain: 4yw2 Chain D Residue 2

Receptor-Ligand Complex Structure

Structure summary

• PDB: 4yw2 Streptococcus pneumoniae NanC: STRUCTURAL INSIGHTS INTO THE SPECIFICITY AND MECHANISM OF A SIALIDASE THAT PRODUCES A SIALIDASE INHIBITOR.
• Resolution: 2.0 Å
• Binding residue (original residue number in PDB): L128 F149 R151 E159 R161 R237
• Binding residue (residue number reindexed from 1): L46 F67 R69 E77 R79 R155
• Annotation score: 4

Enzymatic activity

• Catalytic site (original residue number in PDB): D315 E584 Y695
• Catalytic site (residue number reindexed from 1): D233 E502 Y613
• Enzyme Commision number: 3.2.1.18: exo-alpha-sialidase.

Gene Ontology

Molecular Function

• GO:0004308 exo-alpha-sialidase activity
• GO:0016798 hydrolase activity, acting on glycosyl bonds

Biological Process

• GO:0005975 carbohydrate metabolic process
• GO:0006689 ganglioside catabolic process
• GO:0009313 oligosaccharide catabolic process

Cellular Component

• GO:0005737 cytoplasm
• GO:0016020 membrane
• GO:0043231 intracellular membrane-bounded organelle

External links

• PDB: RCSB:4yw2, PDBe:4yw2, PDBj:4yw2
• PDBsum: 4yw2
• PubMed: 26370075
• UniProt: A0A0H2UQE4