Structure of PDB 6q04 Chain B Binding Site BS01

Receptor Information
>6q04 Chain B (length=1159) Species: 1235996 (Human betacoronavirus 2c EMC/2012) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
TVDVGPDSVKSACIEVDIQQTFFDKTWPRPIDVSKADGIIYPQGRTYSNI
TITYQGLFPYQGDHGDMYVYSAGHATGTTPQKLFVANYSQDVKQFANGFV
VRIGAAANSTGTVIISPSTSATIRKIYPAFMLGSSVGNFSDGKMGRFFNH
TLVLLPDGCGTLLRAFYCILEPRSGNHCPAGNSYTSFATYHTPATDCSDG
NYNRNASLNSFKEYFNLRNCTFMYTYNITEDEILEWFGITQTAQGVHLFS
SRYVDLYGGNMFQFATLPVYDTIKYYSIIPHSIRSIQSDRKAWAAFYVYK
LQPLTFLLDFSVDGYIRRAIDCGFNDLSQLHCSYESFDVESGVYSVSSFE
AKPSGSVVEQAEGVECDFSPLLSGTPPQVYNFKRLVFTNCNYNLTKLLSL
FSVNDFTCSQISPAAIASNCYSSLILDYFSYPLSMKSDLSVSSAGPISQF
NYKQSFSNPTCLILATVPHNLTTITKPLKYSYINKCSRLLSDDRTEVPQL
VNANQYSPCVSIVPSTVWEDGDYYRKQLSPLEGGGWLVASGSTVAMTEQL
QMGFGITVQYGTDTNSVCPKLEFANDTKIASQLGNCVEYSLYGVSGRGVF
QNCTAVGVRQQRFVYDAYQNLVGYYSDDGNYYCLRACVSVPVSVIYDKET
KTHATLFGSVACEHIYGPLQTPVGCVLGLVNSSLFVEDCKLPLGQSLCAL
PDTPGEMRLASIAFNHPIQVDQLNSSYFKLSIPTNFSFGVTQEYIQTTIQ
KVTVDCKQYVCNGFQKCEQLLREYGQFCSKINQALHGANLRQDDSVRNLF
ASVKSSQSSPIIPGFGGDFNLTLLEPVARSAIEDLLFDKVTIADPGYMQG
YDDCMQQGPASARDLICAQYVAGYKVLPPLMDVNMEAAYTSSLLGSIAGV
GWTAGLSSFAAIPFAQSIFYRLNGVGITQQVLSENQKLIANKFNQALGAM
QTGFTTTNEAFQKVQDAVNNNAQALSKLASELSNTFGAISASIGDIIQRL
DPPEQDAQIDRLINGRLTTLNAFVAQQLVRSESAALSAQLAKDKVNECVK
AQSKRSGFCGQGTHIVSFVVNAPNGLYFMHVGYYPSNHIEVVSAYGLCDA
ANPTNCIAPVNGYFIKTEWSYTGSSFYAPEPITSLNTKYVAPQVTYQNIS
TNLPPPLLG
Ligand information
Ligand IDMAN
InChIInChI=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
InChIKeyWQZGKKKJIJFFOK-PQMKYFCFSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0C(C1C(C(C(C(O1)O)O)O)O)O
CACTVS 3.341OC[CH]1O[CH](O)[CH](O)[CH](O)[CH]1O
CACTVS 3.341OC[C@H]1O[C@H](O)[C@@H](O)[C@@H](O)[C@@H]1O
OpenEye OEToolkits 1.5.0C([C@@H]1[C@H]([C@@H]([C@@H]([C@H](O1)O)O)O)O)O
ACDLabs 10.04OC1C(O)C(OC(O)C1O)CO
FormulaC6 H12 O6
Namealpha-D-mannopyranose;
alpha-D-mannose;
D-mannose;
mannose
ChEMBLCHEMBL365590
DrugBank
ZINCZINC000003860903
PDB chain6q04 Chain Z Residue 5 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB6q04 Structures of MERS-CoV spike glycoprotein in complex with sialoside attachment receptors.
Resolution2.5 Å
Binding residue
(original residue number in PDB)		D510 W553
Binding residue
(residue number reindexed from 1)		D493 W536
Annotation score4
Enzymatic activity
Enzyme Commision number ?
Gene Ontology
Molecular Function
GO:0005515 protein binding
Biological Process
GO:0019062 virion attachment to host cell
GO:0019064 fusion of virus membrane with host plasma membrane
GO:0019065 receptor-mediated endocytosis of virus by host cell
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:0061025 membrane fusion
GO:0075509 endocytosis involved in viral entry into host cell
Cellular Component
GO:0016020 membrane
GO:0019031 viral envelope
GO:0020002 host cell plasma membrane
GO:0044173 host cell endoplasmic reticulum-Golgi intermediate compartment membrane
GO:0055036 virion membrane

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:6q04, PDBe:6q04, PDBj:6q04
PDBsum6q04
PubMed31792450
UniProtK0BRG7

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