Structure of PDB 7l56 Chain B Binding Site BS01

Receptor Information
>7l56 Chain B (length=992) Species: 2697049 (Severe acute respiratory syndrome coronavirus 2) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
YTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIDNPVLPFND
GVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCND
PFLFRVYSSANNCTFEYVSKNLREFVFKNIDGYFKIYSKHTPIDLPQGFS
ALEPLVDLPIITRFQTLLAAAYYVGYLQPRTFLLKYNENGTITDAVDCAL
DPLSETKCTLKSFTVEKGIYQTSNFRVQPTESIVRFPNITNLCPFGEVFN
ATRFASVYAWNRKRISNCVADYSVLYNSASFSTFKCYGVSPTKLNDLCFT
NVYADSFVIRGDEVRQIAPGQTGKIADYNYKLPDDFTGCVIAWNSNNLDS
KVGGNYNYLYRLFRKSNLKPFERDISTEIYQAGSTPCNGVEGFNCYFPLQ
SYGFQPTNGVGYQPYRVVVLSFELLHAPATVCGPKKSTNLVKNKCVNFNF
NGLTGTGVLTESNKKFLPFQQFGRDIADTTDAVRDPQTLEILDITPCSFG
GVSVITPGTNTSNQVAVLYQDVNCTEVNVFQTRAGCLIGAEHVNNSYECD
IPIGAGICASYQTQSIIAYTMSLGAENSVAYSNNSIAIPTNFTISVTTEI
LPVSMTKTSVDCTMYICGDSTECSNLLLQYGSFCTQLNRALTGIAVEQDK
NTQEVFAQVKQIYKTPPIKDFGGFNFSQILPDPSKPSKRSFIEDLLFNKV
TLFNGLTVLPPLLTDEMIAQYTSALLAGTITSGWTFGAGAALQIPFAMQM
AYRFNGIGVTQNVLYENQKLIANQFNSAIGKIQDSLSSTASALGKLQDVV
NQNAQALNTLVKQLSSNFGAISSVLNDILSRLDPPEAEVQIDRLITGRLQ
SLQTYVTQQLIRAAEIRASANLAATKMSECVLGQSKRVDFCGKGYHLMSF
PQSAPHGVVFLHVTYVPAQEKNFTTAPAICHDGKAHFPREGVFVSNGTHW
FVTQRNFYEPQIITTDNTFVSGNCDVVIGIVNNTVYDPLQPE
Ligand information
Ligand IDGAL
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-FPRJBGLDSA-N
SMILES
SoftwareSMILES
CACTVS 3.370OC[C@H]1O[C@@H](O)[C@H](O)[C@@H](O)[C@H]1O
OpenEye OEToolkits 1.7.2C(C1C(C(C(C(O1)O)O)O)O)O
CACTVS 3.370OC[CH]1O[CH](O)[CH](O)[CH](O)[CH]1O
ACDLabs 12.01OC1C(O)C(OC(O)C1O)CO
OpenEye OEToolkits 1.7.2C([C@@H]1[C@@H]([C@@H]([C@H]([C@@H](O1)O)O)O)O)O
FormulaC6 H12 O6
Namebeta-D-galactopyranose;
beta-D-galactose;
D-galactose;
galactose
ChEMBLCHEMBL300520
DrugBank
ZINCZINC000002597049
PDB chain7l56 Chain I Residue 6 [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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PDB7l56 Modular basis for potent SARS-CoV-2 neutralization by a prevalent VH1-2-derived antibody class.
Resolution3.6 Å
Binding residue
(original residue number in PDB)		F486 N487 Y489
Binding residue
(residue number reindexed from 1)		F393 N394 Y396
Annotation score4
Enzymatic activity
Enzyme Commision number ?
Gene Ontology
Biological Process
GO:0019064 fusion of virus membrane with host plasma membrane
GO:0039654 fusion of virus membrane with host endosome membrane
GO:0046813 receptor-mediated virion attachment to host cell
GO:0075509 endocytosis involved in viral entry into host cell
Cellular Component
GO:0016020 membrane
GO:0019031 viral envelope
GO:0055036 virion membrane

View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:7l56, PDBe:7l56, PDBj:7l56
PDBsum7l56
PubMed33794145
UniProtP0DTC2|SPIKE_SARS2 Spike glycoprotein (Gene Name=S)

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