Structure of PDB 7ymv Chain B Binding Site BS01

Receptor Information
>7ymv Chain B (length=1166) Species: 1235996 (Human betacoronavirus 2c EMC/2012) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
VDVGPDSVKSACIEVDIQQTFFDKTWPRPIDVSKADGIIYPQGRTYSNIT
ITYQGLFPYQGDHGDMYVYSAGHATGTTPQKLFVANYSQDVKQFANGFVV
RIGAAANSTGTVIISPSTSATIRKIYPAFMLGSSVGNFSDGKMGRFFNHT
LVLLPDGCGTLLRAFYCILEPRSGNHCPAGNSYTSFATYHTPATDCSDGN
YNRNASLNSFKEYFNLRNCTFMYTYNITEDEILEWFGITQTAQGVHLFSS
RYVDLYGGNMFQFATLPVYDTIKYYSIIPHSIRSIQSDRKAWAAFYVYKL
QPLTFLLDFSVDGYIRRAIDCGFNDLSQLHCSYESFDVESGVYSVSSFEA
KPSGSVVEQAEGVECDFSPLLSGTPPQVYNFKRLVFTNCNYNLTKLLSLF
SVNDFTCSQISPAAIASNCYSSLILDYFSYPLSMKSDLSVSSAGPISQFN
YKQSFSNPTCLILATVPHNLTTITKPLKYSYINKCSRLLSDDRTEVPQLV
NANQYSPCVSIVPSTVWEDGDYYRKQLSPLEGGGWLVASGSTVAMTEQLQ
MGFGITVQYGTDTNSVCPKLEFANDTKIASQLGNCVEYSLYGVSGRGVFQ
NCTAVGVRQQRFVYDAYQNLVGYYSDDGNYYCLRACVSVPVSVIYDKETK
THATLFGSVACEHISSTMSQYSRSTRSMYGPLQTPVGCVLGLVNSSLFVE
DCKLPLGQSLCALPDTPGEMRLASIAFNHPIQVDQLNSSYFKLSIPTNFS
FGVTQEYIQTTIQKVTVDCKQYVCNGFQKCEQLLREYGQFCSKINQALHG
ANLRQDDSVRNLFASVKSSQSSPIIPGFGGDFNLTLLEPVARSAIEDLLF
DKVTIADPGYMQGYDDCMQQLICAQYVAGYKVLPPLMDVNMEAAYTSSLL
GSIAGVGWTAGLSSFAAIPFAQSIFYRLNGVGITQQVLSENQKLIANKFN
QALGAMQTGFTTTNEAFQKVQDAVNNNAQALSKLASELSNTFGAISASIG
DIIQRLDPPEQDAQIDRLINGRLTTLNAFVAQQLVRSESAALSAQLAKDK
VNECVKAQSKRSGFCGQGTHIVSFVVNAPNGLYFMHVGYYPSNHIEVVSA
YGLCDAANPTNCIAPVNGYFIKTNNEWSYTGSSFYAPEPITSLNTKYVAP
QVTYQNISTNLPPPLL
Ligand information
Ligand IDBMA
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-RWOPYEJCSA-N
SMILES
SoftwareSMILES
CACTVS 3.341OC[C@H]1O[C@@H](O)[C@@H](O)[C@@H](O)[C@@H]1O
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
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
Namebeta-D-mannopyranose;
beta-D-mannose;
D-mannose;
mannose
ChEMBL
DrugBank
ZINCZINC000003830679
PDB chain7ymv Chain N Residue 3 [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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PDB7ymv GlycoSHIELD: a versatile pipeline to assess glycan impact on protein structures
Resolution6.74 Å
Binding residue
(original residue number in PDB)		L273 Y274
Binding residue
(residue number reindexed from 1)		L255 Y256
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:7ymv, PDBe:7ymv, PDBj:7ymv
PDBsum7ymv
PubMed38428397
UniProtK0BRG7

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