Structure of PDB 5tip Chain D Binding Site BS02

Receptor Information

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

AGGLSQLVAYGAQDVYLTGNPQITFFKTVYRRYTNFAIESIQQTINGSVG
FGNKVSTQISRNGDLITDIVVEFVLTKGGNGGTTYYPAEELLQDVELEIG
GQRIDKHYNDWFRTYDALFRMNDDRYNYRRMTDWVNNELVGAQKRFYVPL
IFFFNQTPGLALPLIALQYHEVKLYFTLASQVQGVNYNGSSAIAGAAQPT
MSVWVDYIFLDTQERTRFAQLPHEYLIEQLQFTGSETATPSATTQASQNI
RLNFNHPTKYLAWNFNNPTNYGQYTALANIPGACSGAGTAAATVTTPDYG
NTGTYNEQLAVLDSAKIQLNGQDRFATRKGSYFNKVQPYQSIGGVTPAGV
YLYSFALKPAGRQPSGTCNFSRIDNATLSLTYKTCSIDATSPAAVLGNTE
TVTANTATLLTALNIYAKNYNVLRIMSGMGGLAYAN

Ligand information

• Ligand ID: FUC
• 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-SXUWKVJYSA-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: CC1C(C(C(C(O1)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
  CACTVS 3.341: C[CH]1O[CH](O)[CH](O)[CH](O)[CH]1O
• Formula: C6 H12 O5
• Name: alpha-L-fucopyranose;
  alpha-L-fucose;
  6-deoxy-alpha-L-galactopyranose;
  L-fucose;
  fucose
• ChEMBL: CHEMBL1232862
• DrugBank: DB04473
• ZINC: ZINC000001532814
• PDB chain: 5tip Chain Q Residue 2

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): G82 N138
• Binding residue (residue number reindexed from 1): G81 N137
• 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)