Structure of PDB 7yl6 Chain A Binding Site BS01

Receptor Information

>7yl6 Chain A (length=472) Species: 1360 (Lactococcus lactis subsp. lactis)

TSRDITVYPKDFLTYFQRNGSAAGFDYDLATYTQTLTPNKASQAGNVTLK
TKVDMSQNFTFTGKINLGDKAQNAGGADGVGFLFHPGDTNVVGAPGGAAG
IGGVNGAFGFKLDTYYNGVGENSFTPDPSNFKGKPFGAFVDGLNGQAKTI
ASSAQSISEPSNNNFVDFTMSYNGATKVMSVTYGGQTWTQDVSSFVGTNQ
AMSFSIAASTGAFMNLQQLRNVNFTYTVAQGTVIANYVDEQGNTIAQQET
TSGDIDTPYVTSQKTIPGYTFKASNGAATSGNYAANDQTVNYVYTRNQGS
IDVTYIDQTTGQTLSKKDLSGGTGDSSNYTTTDTIKSYTDAGYELVSDNY
PSGGTVFTDTAQHYVVNLKQKLVVSSEQKQVNETIQYVYEDGSKAADDYN
APPLNFTRSVTTNQVTGEKTYGDWQAQNGDSFGEVVSPTIKGETADQLKI
DAISGITANSADIQKKVVYKRN

Ligand information

• Ligand ID: MAN
• InChI: InChI=1S/C6H12O6/c7-1-2-3(8)4(9)5(10)6(11)12-2/h2-11H,1H2/t2-,3-,4+,5+,6+/m1/s1
• InChIKey: WQZGKKKJIJFFOK-PQMKYFCFSA-N
• SMILES:
  OpenEye OEToolkits 1.5.0: C(C1C(C(C(C(O1)O)O)O)O)O
  CACTVS 3.341: OC[CH]1O[CH](O)[CH](O)[CH](O)[CH]1O
  CACTVS 3.341: OC[C@H]1O[C@H](O)[C@@H](O)[C@@H](O)[C@@H]1O
  OpenEye OEToolkits 1.5.0: C([C@@H]1[C@H]([C@@H]([C@@H]([C@H](O1)O)O)O)O)O
  ACDLabs 10.04: OC1C(O)C(OC(O)C1O)CO
• Formula: C6 H12 O6
• Name: alpha-D-mannopyranose;
  alpha-D-mannose;
  D-mannose;
  mannose
• ChEMBL: CHEMBL365590
• ZINC: ZINC000003860903
• PDB chain: 7yl6 Chain C Residue 1

Receptor-Ligand Complex Structure

Structure summary

• PDB: 7yl6 Cell-surface protein YwfG of Lactococcus lactis binds to alpha-1,2-linked mannose.
• Resolution: 2.95 Å
• Binding residue (original residue number in PDB): D117 Y154 N156 G250 A251 F252
• Binding residue (residue number reindexed from 1): D78 Y115 N117 G211 A212 F213
• Annotation score: 4

External links

• PDB: RCSB:7yl6, PDBe:7yl6, PDBj:7yl6
• PDBsum: 7yl6
• PubMed: 36602978
• UniProt: S6FKX6