Structure of PDB 7nyd Chain D Binding Site BS01

Receptor Information
>7nyd Chain D (length=487) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
VTLMPIDCELSSWSSWTTCDPCQKKRYRYAYLLQPSQFHGEPCNFSDKEV
EDCVTNRPCRSQVRCEGFVCAQTGRCVNRRLLCNGDNDCGDQSDEANCRR
IYKKCQHEMDQYWGIGSLASGINLFTNSFEGPVLDHRYYAGGCSPHYILN
TRFRKPYNVESYTPQTQGKYEFILKEYESYSDFERNVTEKMASKDRGKHY
IRRTKRFSHTKSVFLHARSDLEVAHYKLKPRSLMLHYEFLQRVKRLPLEY
SYGEYRDLFRDFGTHYITEAVLGGIYEYTLVMNKEAMERGDYTLNNVHAR
GILNEIKDRNKRDTMVEDLVVLVRGGASEHITTLAYQELPTADLMQEWGD
AVQYNPAIIKVKVEPLYELVTATDFAYSSTVRQNMKQALEEFQKEVSSCH
CAPCQGNGVPVLKGSRCDCICPVGSQGLACEVSYRKNTPIDGKWNCWSNW
SSCSGRRKTRQRQCNNPPPQNGGSPCSGPASETLDCS
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 chain7nyd Chain D Residue 601 [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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PDB7nyd Structural basis of soluble membrane attack complex packaging for clearance.
Resolution3.27 Å
Binding residue
(original residue number in PDB)		E440 K444 N499 W500
Binding residue
(residue number reindexed from 1)		E390 K394 N449 W450
Annotation score4
Enzymatic activity
Enzyme Commision number ?
Gene Ontology
Molecular Function
GO:0044877 protein-containing complex binding
Biological Process
GO:0006955 immune response
GO:0006956 complement activation
GO:0006957 complement activation, alternative pathway
GO:0006958 complement activation, classical pathway
GO:0031640 killing of cells of another organism
GO:0050778 positive regulation of immune response
Cellular Component
GO:0005576 extracellular region
GO:0005579 membrane attack complex
GO:0005615 extracellular space
GO:0005886 plasma membrane
GO:0016020 membrane
GO:0070062 extracellular exosome
GO:1903561 extracellular vesicle

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:7nyd, PDBe:7nyd, PDBj:7nyd
PDBsum7nyd
PubMed34667172
UniProtP07358|CO8B_HUMAN Complement component C8 beta chain (Gene Name=C8B)

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