Structure of PDB 1m7i Chain B Binding Site BS01

Receptor Information

>1m7i Chain B (length=220) Species: 10090 (Mus musculus)

EVKVEESGGGLVQPGGSMKLSCVASGFTFSNYWMEWVRQSPEKGLEWVAE
IRLKSNNYATHYAESVKGRFTISRDDSKSSVYLQMNNLRAEDTGIYYCTR
GGAVGAMDYWGQGTSVTVSSATTTAPSVYPLVPGCSDTSGSSVTLGCLVK
GYFPEPVTVKWNYGALSSGVRTVSSVLQSGFYSLSSLVTVPSSTWPSQTV
ICNVAHPASKVDLIKEPSGP

Ligand information

• Ligand ID: RAM
• InChI: InChI=1S/C6H12O5/c1-2-3(7)4(8)5(9)6(10)11-2/h2-10H,1H3/t2-,3-,4+,5+,6+/m0/s1
• InChIKey: SHZGCJCMOBCMKK-HGVZOGFYSA-N
• SMILES:
  CACTVS 3.341: C[C@@H]1O[C@@H](O)[C@H](O)[C@H](O)[C@H]1O
  ACDLabs 10.04: OC1C(O)C(OC(O)C1O)C
  OpenEye OEToolkits 1.5.0: C[C@H]1[C@@H]([C@H]([C@H]([C@@H](O1)O)O)O)O
  OpenEye OEToolkits 1.5.0: CC1C(C(C(C(O1)O)O)O)O
  CACTVS 3.341: C[CH]1O[CH](O)[CH](O)[CH](O)[CH]1O
• Formula: C6 H12 O5
• Name: alpha-L-rhamnopyranose;
  alpha-L-rhamnose;
  6-deoxy-alpha-L-mannopyranose;
  L-rhamnose;
  rhamnose
• ZINC: ZINC000003861280
• PDB chain: 1m7i Chain C Residue 5

Receptor-Ligand Complex Structure

Structure summary

• PDB: 1m7i Molecular Recognition of Oligosaccharide Epitopes by a Monoclonal Fab Specific for Shigella flexneri Y Lipopolysaccharide: X-ray Structures and Thermodynamics
• Resolution: 2.5 Å
• Binding residue (original residue number in PDB): W33 G95
• Binding residue (residue number reindexed from 1): W33 G101
• Annotation score: 4
• Binding affinity: PDBbind-CN: -logKd/Ki=5.40,Kd=4.0uM

Gene Ontology

Molecular Function

• GO:0003823 antigen binding

Biological Process

• GO:0002250 adaptive immune response
• GO:0016064 immunoglobulin mediated immune response

Cellular Component

• GO:0019814 immunoglobulin complex

External links

• PDB: RCSB:1m7i, PDBe:1m7i, PDBj:1m7i
• PDBsum: 1m7i
• PubMed: 12427018
• UniProt: P01801|HVM32_MOUSE Ig heavy chain V-III region J606