Structure of PDB 6zp2 Chain A Binding Site BS02

Receptor Information

>6zp2 Chain A (length=1097) Species: 2697049 (Severe acute respiratory syndrome coronavirus 2)

QCVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVT
WFHAIHVKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLI
VNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFE
YVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQG
FSALEPLVDLPIGINITRFQTLLALHRSYLTPGDSSSGWTAGAAAYYVGY
LQPRTFLLKYNENGTITDAVDCALDPLSETKCTLKSFTVEKGIYQTSNFR
VQPTESIVRFPNITNLCPFGEVFNATRFASVYAWNRKRISNCVADYSVLY
NSASFSTFKCYGVSPTKLNDLCFTNVYADSFVIRGDEVRQIAPGQTGKIA
DYNYKLPDDFTGCVIAWNSNNLDSKVGGNYNYLYRLFRKSNLKPFERDIS
TEIYQAGSTPCNGVEGFNCYFPLQSYGFQPTNGVGYQPYRVVVLSFELLH
APATVCGPKKSTNLVKNKCVNFNFNGLTGTGVLTESNKKFLPFQQFGRDI
ADTTDAVRDPQTLEILDITPCSFGGVSVITPGTNTSNQVAVLYQDVNCTT
WRVYSTGSNVFQTRAGCLIGAEHVNNSYECDIPIGAGICASYQTSQSIIA
YTMSLGAENSVAYSNNSIAIPTNFTISVTTEILPVSMTKTSVDCTMYICG
DSTECSNLLLQYGSFCTQLNRALTGIAVEQDKNTQEVFAQVKQIYKTPPI
KDFGGFNFSQILPDPSKPSKRSFIEDLLFNKVTLADAGFIKQYGDCLGDI
AARDLICAQKFNGLTVLPPLLTDEMIAQYTSALLAGTITSGWTFGAGAAL
QIPFAMQMAYRFNGIGVTQNVLYENQKLIANQFNSAIGKIQDSLSSTASA
LGKLQDVVNQNAQALNTLVKQLSSNFGAISSVLNDILSRLDPPEAEVQID
RLITGRLQSLQTYVTQQLIRAAEIRASANLAATKMSECVLGQSKRVDFCG
KGYHLMSFPQSAPHGVVFLHVTYVPAQEKNFTTAPAICHDGKAHFPREGV
FVSNGTHWFVTQRNFYEPQIITTDNTFVSGNCDVVIGIVNNTVYDPL

Ligand information

• Ligand ID: EIC
• InChI: InChI=1S/C18H32O2/c1-2-3-4-5-6-7-8-9-10-11-12-13-14-15-16-17-18(19)20/h6-7,9-10H,2-5,8,11-17H2,1H3,(H,19,20)/b7-6-,10-9-
• InChIKey: OYHQOLUKZRVURQ-HZJYTTRNSA-N
• SMILES:
  CACTVS 3.341: CCCCCC=CCC=CCCCCCCCC(O)=O
  CACTVS 3.341: CCCCC/C=C\C\C=C/CCCCCCCC(O)=O
  OpenEye OEToolkits 1.5.0: CCCCC\C=C/C\C=C/CCCCCCCC(=O)O
  OpenEye OEToolkits 1.5.0: CCCCCC=CCC=CCCCCCCCC(=O)O
  ACDLabs 10.04: O=C(O)CCCCCCC\C=C/C\C=C/CCCCC
• Formula: C18 H32 O2
• Name: LINOLEIC ACID;
  9,12-LINOLEIC ACID
• ChEMBL: CHEMBL267476
• DrugBank: DB14104
• ZINC: ZINC000004474613
• PDB chain: 6zp2 Chain A Residue 2112

Receptor-Ligand Complex Structure

Structure summary

• PDB: 6zp2 A thermostable, closed SARS-CoV-2 spike protein trimer.
• Resolution: 3.1 Å
• Binding residue (original residue number in PDB): P337 F338 I358 Y365 Y369 F374 F377 F392 I434 F515
• Binding residue (residue number reindexed from 1): P318 F319 I339 Y346 Y350 F355 F358 F373 I415 F496
• Annotation score: 4

Gene Ontology

Molecular Function

• GO:0005515 protein binding
• GO:0039660 structural constituent of virion
• GO:0042802 identical protein binding
• GO:0046789 host cell surface receptor binding
• GO:0048018 receptor ligand activity

Biological Process

• GO:0007165 signal transduction
• GO:0019062 virion attachment to host cell
• GO:0019064 fusion of virus membrane with host plasma membrane
• GO:0019081 viral translation
• GO:0039587 suppression by virus of host tetherin activity
• GO:0039654 fusion of virus membrane with host endosome membrane
• GO:0046598 positive regulation of viral entry into host cell
• GO:0046718 symbiont entry into host cell
• GO:0046813 receptor-mediated virion attachment to host cell
• GO:0052170 symbiont-mediated suppression of host innate immune response
• GO:0061025 membrane fusion
• GO:0075509 endocytosis involved in viral entry into host cell
• GO:0098670 entry receptor-mediated virion attachment to host cell

Cellular Component

• GO:0005886 plasma membrane
• GO:0016020 membrane
• GO:0019031 viral envelope
• GO:0020002 host cell plasma membrane
• GO:0043655 host extracellular space
• GO:0044173 host cell endoplasmic reticulum-Golgi intermediate compartment membrane
• GO:0044228 host cell surface
• GO:0055036 virion membrane

External links

• PDB: RCSB:6zp2, PDBe:6zp2, PDBj:6zp2
• PDBsum: 6zp2
• PubMed: 32737467
• UniProt: P0DTC2|SPIKE_SARS2 Spike glycoprotein (Gene Name=S)