Structure of PDB 6er3 Chain B Binding Site BS01

Receptor Information

>6er3 Chain B (length=185) Species: 411470 (Mediterraneibacter gnavus ATCC 29149)

GSVLQKEGIEISEGTGYDLSKEPGAATVKALEQGTIVISYKTTSENAIQS
LLSVGNGTKGNQDRHFHLYITNAGGVGMELRNTDGEFKYTLDCPAAVRGR
VSNTVALKADKENKQYKLFANGELIATLDQEAFKFISDITGVDNVMLGGT
MRQGTVAYPFGGSIERMQVYRDVLSDDELIAVTGI

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: 6er3 Chain D Residue 2

Receptor-Ligand Complex Structure

Structure summary

• PDB: 6er3 Unravelling the specificity and mechanism of sialic acid recognition by the gut symbiont Ruminococcus gnavus.
• Resolution: 1.37 Å
• Binding residue (original residue number in PDB): I54 E85 R87 K94 R163 Y169
• Binding residue (residue number reindexed from 1): I48 E79 R81 K88 R152 Y158
• Annotation score: 4
• Binding affinity: PDBbind-CN: -logKd/Ki=3.24,Kd=0.57mM

Gene Ontology

Molecular Function

• GO:0004308 exo-alpha-sialidase activity

Biological Process

• GO:0005975 carbohydrate metabolic process

External links

• PDB: RCSB:6er3, PDBe:6er3, PDBj:6er3
• PDBsum: 6er3
• PubMed: 29259165
• UniProt: A7B557