Structure of PDB 8a1d Chain D Binding Site BS01

Receptor Information
>8a1d Chain D (length=533) Species: 10090 (Mus musculus) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
TGFQICKNALKLPVLEVLPGGGWDNLRNVDMGRVMDLTYTNCKTTEDGQY
IIPDEVYTIPQKESNLEMNSEVLESWMNYQSTTSLSINTELALFSRVNGK
FSTEFQRMKTLQVKDQAVTTRVQVRNRIYTVKTTPTSELSLGFTKALMDI
CDQLEKNQTKMATYLAELLILNYGTHVITSVDAGAALVQEDHVRSSFLLD
NQNSQNTVTASAGIAFLNIVNFKVETDYISQTSLTKDYLSNRTNSRVQSF
GGVPFYPGITLETWQKGITNHLVAIDRAGLPLHFFIKPDKLPGLPGPLVK
KLSKTVETAVRHYYTFNFTFGGVYQECTELSGDVLCQNLEQKNLLTGDFS
CPPGYSPVHLLSQTHEEGYSRLECKKKCTLKIFCKTVCEDVFRVAKAEFR
AYWCVAAGQVPDNSGLLFGGVFTDKTINPMTNAQSCPAGYIPLNLFESLK
VCVSLDYELGFKFSVPFGGFFSCIMGNPLVNAPSLKKCPGGFSQHLAVIS
DGCQVSYCVKAGIFTGGSLLPVRLPPYTKPPLM
Ligand information
Ligand IDMA4
InChIInChI=1S/C24H44O11/c25-12-15-17(27)18(28)20(30)24(33-15)35-22-16(13-26)34-23(21(31)19(22)29)32-11-7-2-1-4-8-14-9-5-3-6-10-14/h14-31H,1-13H2/t15-,16-,17-,18+,19-,20-,21-,22-,23-,24-/m1/s1
InChIKeyWUCWJXGMSXTDAV-QKMCSOCLSA-N
SMILES
SoftwareSMILES
CACTVS 3.341OC[CH]1O[CH](O[CH]2[CH](O)[CH](O)[CH](OCCCCCCC3CCCCC3)O[CH]2CO)[CH](O)[CH](O)[CH]1O
ACDLabs 10.04O(CCCCCCC1CCCCC1)C3OC(C(OC2OC(CO)C(O)C(O)C2O)C(O)C3O)CO
OpenEye OEToolkits 1.5.0C1CCC(CC1)CCCCCCOC2C(C(C(C(O2)CO)OC3C(C(C(C(O3)CO)O)O)O)O)O
OpenEye OEToolkits 1.5.0C1CCC(CC1)CCCCCCO[C@H]2[C@@H]([C@H]([C@@H]([C@H](O2)CO)O[C@@H]3[C@@H]([C@H]([C@@H]([C@H](O3)CO)O)O)O)O)O
CACTVS 3.341OC[C@H]1O[C@H](O[C@H]2[C@H](O)[C@@H](O)[C@H](OCCCCCCC3CCCCC3)O[C@@H]2CO)[C@H](O)[C@@H](O)[C@@H]1O
FormulaC24 H44 O11
NameCYCLOHEXYL-HEXYL-BETA-D-MALTOSIDE
ChEMBL
DrugBankDB03472
ZINCZINC000016051503
PDB chain8a1d Chain D Residue 702 [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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PDB8a1d Cryo-EM structures of perforin-2 in isolation and assembled on a membrane suggest a mechanism for pore formation.
Resolution3.0 Å
Binding residue
(original residue number in PDB)		Y266 G426 Y427 S428
Binding residue
(residue number reindexed from 1)		Y238 G368 Y369 S370
Annotation score1
Enzymatic activity
Enzyme Commision number ?
Gene Ontology
Molecular Function
GO:0022829 wide pore channel activity
GO:0140911 pore-forming activity
Biological Process
GO:0002250 adaptive immune response
GO:0002468 dendritic cell antigen processing and presentation
GO:0002478 antigen processing and presentation of exogenous peptide antigen
GO:0042590 antigen processing and presentation of exogenous peptide antigen via MHC class I
GO:0042742 defense response to bacterium
GO:0045087 innate immune response
GO:0050829 defense response to Gram-negative bacterium
GO:0050830 defense response to Gram-positive bacterium
GO:0055085 transmembrane transport
GO:0140367 antibacterial innate immune response
Cellular Component
GO:0016020 membrane
GO:0030670 phagocytic vesicle membrane
GO:0031410 cytoplasmic vesicle
GO:0036019 endolysosome
GO:0045335 phagocytic vesicle
GO:0061474 phagolysosome membrane

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:8a1d, PDBe:8a1d, PDBj:8a1d
PDBsum8a1d
PubMed36245269
UniProtA1L314|MPEG1_MOUSE Macrophage-expressed gene 1 protein (Gene Name=Mpeg1)

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