Structure of PDB 2r1y Chain B Binding Site BS01

Receptor Information

>2r1y Chain B (length=216) Species: 10090 (Mus musculus)

EVKLVESGGGLVQSGGSLRLSCATSGFTFTDYYMSWVRQPPGKALEWLGF
IRNKANGYTTEYSPSVKGRFTISRDNSQSILYLQMNTLRAEDSATYYCAR
DHDGYYERFSYWGQGTLVTVSAAKTTPPSVYPLAPNSMVTLGCLVKGYFP
EPVTVTWNSGSLSSGVHTFPAVLQSDLYTLSSSVTVPSSTWPSETVTCNV
AHPASSTKVDKKIVPR

Ligand information

• Ligand ID: KDR
• InChI: InChI=1S/C11H18O7/c1-2-3-17-11(6-13)4-7(14)9(16)10(18-11)8(15)5-12/h2,6-10,12,14-16H,1,3-5H2/t7-,8-,9-,10-,11-/m1/s1
• InChIKey: FRBOGERKQAMFNA-ISUQUUIWSA-N
• SMILES:
  OpenEye OEToolkits 1.5.0: C=CCOC1(CC(C(C(O1)C(CO)O)O)O)C=O
  OpenEye OEToolkits 1.5.0: C=CCO[C@@]1(C[C@H]([C@H]([C@H](O1)[C@@H](CO)O)O)O)C=O
  CACTVS 3.341: OC[C@@H](O)[C@H]1O[C@@](C[C@@H](O)[C@H]1O)(OCC=C)C=O
  CACTVS 3.341: OC[CH](O)[CH]1O[C](C[CH](O)[CH]1O)(OCC=C)C=O
  ACDLabs 10.04: O=CC1(OC\C=C)OC(C(O)CO)C(O)C(O)C1
• Formula: C11 H18 O7
• Name: prop-2-en-1-yl 3-deoxy-alpha-D-manno-octos-2-ulopyranoside;
  prop-2-en-1-yl 3-deoxy-alpha-D-manno-octos-2-uloside;
  prop-2-en-1-yl 3-deoxy-D-manno-octos-2-uloside;
  prop-2-en-1-yl 3-deoxy-manno-octos-2-uloside
• ZINC: ZINC000058638844
• PDB chain: 2r1y Chain C Residue 1

Receptor-Ligand Complex Structure

Structure summary

• PDB: 2r1y Exploration of specificity in germline monoclonal antibody recognition of a range of natural and synthetic epitopes.
• Resolution: 1.6 Å
• Binding residue (original residue number in PDB): Y33 N52D
• Binding residue (residue number reindexed from 1): Y33 N56
• Annotation score: 1

Gene Ontology

Molecular Function

• GO:0046872 metal ion binding

Biological Process

• GO:0002250 adaptive immune response

Cellular Component

• GO:0019814 immunoglobulin complex

External links

• PDB: RCSB:2r1y, PDBe:2r1y, PDBj:2r1y
• PDBsum: 2r1y
• PubMed: 18272175
• UniProt: A2NU21