Structure of PDB 5tip Chain A Binding Site BS04

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: XYP
• InChI: InChI=1S/C5H10O5/c6-2-1-10-5(9)4(8)3(2)7/h2-9H,1H2/t2-,3+,4-,5-/m1/s1
• InChIKey: SRBFZHDQGSBBOR-KKQCNMDGSA-N
• SMILES:
  OpenEye OEToolkits 1.5.0: C1C(C(C(C(O1)O)O)O)O
  CACTVS 3.341: O[C@@H]1CO[C@@H](O)[C@H](O)[C@H]1O
  OpenEye OEToolkits 1.5.0: C1[C@H]([C@@H]([C@H]([C@@H](O1)O)O)O)O
  CACTVS 3.341: O[CH]1CO[CH](O)[CH](O)[CH]1O
  ACDLabs 10.04: OC1C(O)COC(O)C1O
• Formula: C5 H10 O5
• Name: beta-D-xylopyranose;
  beta-D-xylose;
  D-xylose;
  xylose
• ZINC: ZINC000001529215
• PDB chain: 5tip Chain F Residue 3

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): N81 G82 L140
• Binding residue (residue number reindexed from 1): N80 G81 L139
• 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)