Structure of PDB 5tip Chain A Binding Site BS05

Receptor Information

>5tip Chain A (length=436) Species: 10506 (Paramecium bursaria Chlorella virus 1)

AGGLSQLVAYGAQDVYLTGNPQITFFKTVYRRYTNFAIESIQQTINGSVG
FGNKVSTQISRNGDLITDIVVEFVLTKGGNGGTTYYPAEELLQDVELEIG
GQRIDKHYNDWFRTYDALFRMNDDRYNYRRMTDWVNNELVGAQKRFYVPL
IFFFNQTPGLALPLIALQYHEVKLYFTLASQVQGVNYNGSSAIAGAAQPT
MSVWVDYIFLDTQERTRFAQLPHEYLIEQLQFTGSETATPSATTQASQNI
RLNFNHPTKYLAWNFNNPTNYGQYTALANIPGACSGAGTAAATVTTPDYG
NTGTYNEQLAVLDSAKIQLNGQDRFATRKGSYFNKVQPYQSIGGVTPAGV
YLYSFALKPAGRQPSGTCNFSRIDNATLSLTYKTCSIDATSPAAVLGNTE
TVTANTATLLTALNIYAKNYNVLRIMSGMGGLAYAN

Ligand information

• Ligand ID: GLA
• 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-PHYPRBDBSA-N
• SMILES:
  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(C1C(C(C(C(O1)O)O)O)O)O
  OpenEye OEToolkits 1.5.0: C([C@@H]1[C@@H]([C@@H]([C@H]([C@H](O1)O)O)O)O)O
  CACTVS 3.341: OC[CH]1O[CH](O)[CH](O)[CH](O)[CH]1O
  ACDLabs 10.04: OC1C(O)C(OC(O)C1O)CO
• Formula: C6 H12 O6
• Name: alpha-D-galactopyranose;
  alpha-D-galactose;
  D-galactose;
  galactose;
  ALPHA D-GALACTOSE
• ChEMBL: CHEMBL1233058
• ZINC: ZINC000000901155
• PDB chain: 5tip Chain F Residue 8

Receptor-Ligand Complex Structure

Structure summary

• PDB: 5tip Structure of the chlorovirus PBCV-1 major capsid glycoprotein determined by combining crystallographic and carbohydrate molecular modeling approaches.
• Resolution: 2.0 Å
• Binding residue (original residue number in PDB): G83 S286 G287 D299
• Binding residue (residue number reindexed from 1): G82 S285 G286 D298
• Annotation score: 4

Gene Ontology

Molecular Function

• GO:0005198 structural molecule activity
• GO:0008289 lipid binding

Cellular Component

• GO:0019028 viral capsid

External links

• PDB: RCSB:5tip, PDBe:5tip, PDBj:5tip
• PDBsum: 5tip
• PubMed: 29255015
• UniProt: P30328|MCP_PBCV1 Major capsid protein (Gene Name=A430L)