4BIK | pdb_00004bik

Structure of a disulfide locked mutant of Intermedilysin with human CD59

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Pharos: Disease Associations
Membrane Protein Annotation: OPM

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	MAC/CDC-like	8052024	3002081	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	CDC membrane-sensing domain-like	8052023	3000285	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	CDC membrane-sensing domain-like	8052023	3000285	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	MAC/CDC-like	8052024	3002081	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Snake toxin-like	8034633	3000545	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Snake toxin-like	8034633	3000545	SCOP2B (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A	Thiol_cytolys_C	e4bikA1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Perfringolysin O beta sandwich domain (From Topology)	T: Perfringolysin O beta sandwich domain	F: Thiol_cytolys_C	ECOD (1.6)
A	Thiol_cytolysin	e4bikA2	A: beta complex topology	X: Membrane attack complex/perforin (MACPF) and cholesterol-dependent cytolysin (CDC) domains (From Topology)	H: Membrane attack complex/perforin (MACPF) and cholesterol-dependent cytolysin (CDC) domains (From Topology)	T: Membrane attack complex/perforin (MACPF) and cholesterol-dependent cytolysin (CDC) domains	F: Thiol_cytolysin	ECOD (1.6)
C	Thiol_cytolys_C	e4bikC1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Perfringolysin O beta sandwich domain (From Topology)	T: Perfringolysin O beta sandwich domain	F: Thiol_cytolys_C	ECOD (1.6)
C	Thiol_cytolysin	e4bikC2	A: beta complex topology	X: Membrane attack complex/perforin (MACPF) and cholesterol-dependent cytolysin (CDC) domains (From Topology)	H: Membrane attack complex/perforin (MACPF) and cholesterol-dependent cytolysin (CDC) domains (From Topology)	T: Membrane attack complex/perforin (MACPF) and cholesterol-dependent cytolysin (CDC) domains	F: Thiol_cytolysin	ECOD (1.6)
B	UPAR_LY6	e4bikB1	A: few secondary structure elements	X: Snake toxin-like (From Topology)	H: Snake toxin-like (From Topology)	T: Snake toxin-like	F: UPAR_LY6	ECOD (1.6)
D	UPAR_LY6	e4bikD1	A: few secondary structure elements	X: Snake toxin-like (From Topology)	H: Snake toxin-like (From Topology)	T: Snake toxin-like	F: UPAR_LY6	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.90.840.10	Alpha Beta	Alpha-Beta Complex	HIV-1 Reverse Transcriptase	Chain A, domain 3	CATH (4.3.0)
A	3.30.1040.20	Alpha Beta	2-Layer Sandwich	Carboxypeptidase Inhibitor	Chain A	CATH (4.3.0)
A	3.40.30.40	Alpha Beta	3-Layer(aba) Sandwich	Glutaredoxin	Perfringolysin	CATH (4.3.0)
A	2.60.40.1430	Mainly Beta	Sandwich	Immunoglobulin-like	Perfringolysin, domain 4	CATH (4.3.0)
C	3.90.840.10	Alpha Beta	Alpha-Beta Complex	HIV-1 Reverse Transcriptase	Chain A, domain 3	CATH (4.3.0)
C	3.30.1040.20	Alpha Beta	2-Layer Sandwich	Carboxypeptidase Inhibitor	Chain A	CATH (4.3.0)
C	3.40.30.40	Alpha Beta	3-Layer(aba) Sandwich	Glutaredoxin	Perfringolysin	CATH (4.3.0)
C	2.60.40.1430	Mainly Beta	Sandwich	Immunoglobulin-like	Perfringolysin, domain 4	CATH (4.3.0)
B	2.10.60.10	Mainly Beta	Ribbon	CD59	CD59	CATH (4.3.0)
D	2.10.60.10	Mainly Beta	Ribbon	CD59	CD59	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, C	PF17440	Thiol-activated cytolysin beta sandwich domain (Thiol_cytolys_C)	Thiol-activated cytolysin beta sandwich domain	This domain has an immunoglobulin like fold. It is found at the C-terminus of the thiol-activated cytolsin protein.	Domain
A, C	PF01289	Thiol-activated cytolysin (Thiol_cytolysin)	Thiol-activated cytolysin	-	Family
B, D	PF00021	u-PAR/Ly-6 domain (UPAR_LY6)	u-PAR/Ly-6 domain	This extracellular disulphide bond rich domain is related to Pfam:PF00087.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, C	INTERMEDILYSIN	sterol binding binding alcohol binding steroid binding lipid binding cholesterol binding small molecule binding cation binding ion binding metal ion binding toxin activity	biological process involved in interspecies interaction between organisms cellular process disruption of cell in another organism disruption of anatomical structure in another organism killing of cells of another organism cell killing	cellular anatomical structure membrane host cell plasma membrane host cellular component host cell part host cell membrane extracellular region
B, D	CD59 GLYCOPROTEIN	protein binding binding complement binding	multicellular organismal process regulation of body fluid levels wound healing response to stimulus hemostasis biological regulation blood coagulation response to stress coagulation regulation of biological quality response to wounding regulation of biological process regulation of cellular process regulation of complement-dependent cytotoxicity multicellular organismal process regulation of body fluid levels wound healing response to stimulus hemostasis biological regulation blood coagulation response to stress coagulation regulation of biological quality response to wounding regulation of biological process regulation of cellular process regulation of complement-dependent cytotoxicity cellular process regulation of cell killing complement-dependent cytotoxicity cell killing cellular response to stimulus cell surface receptor signaling pathway signaling signal transduction cell communication regulation of humoral immune response regulation of immune effector process humoral immune response positive regulation of biological process negative regulation of biological process negative regulation of complement activation positive regulation of response to stimulus complement activation positive regulation of immune response regulation of immune system process positive regulation of immune system process activation of membrane attack complex immune response negative regulation of response to stimulus negative regulation of immune response negative regulation of immune effector process negative regulation of humoral immune response immune effector process regulation of response to stimulus negative regulation of immune system process immune system process negative regulation of activation of membrane attack complex regulation of immune response regulation of activation of membrane attack complex regulation of complement activation activation of immune response	membrane-bounded organelle intracellular anatomical structure tertiary granule membrane membrane intracellular vesicle intracellular membrane-bounded organelle endomembrane system tertiary granule intracellular organelle cytoplasmic vesicle membrane cellular anatomical structure bounding membrane of organelle vesicle membrane cytoplasmic vesicle membrane-bounded organelle intracellular anatomical structure tertiary granule membrane membrane intracellular vesicle intracellular membrane-bounded organelle endomembrane system tertiary granule intracellular organelle cytoplasmic vesicle membrane cellular anatomical structure bounding membrane of organelle vesicle membrane cytoplasmic vesicle organelle secretory granule secretory vesicle cytoplasm vesicle organelle membrane secretory granule membrane anchoring junction cell junction focal adhesion cell-substrate junction specific granule membrane specific granule cell periphery cell surface plasma membrane external side of plasma membrane side of membrane Golgi membrane Golgi apparatus endoplasmic reticulum-Golgi intermediate compartment membrane endoplasmic reticulum-Golgi intermediate compartment extracellular exosome extracellular vesicle extracellular organelle extracellular region extracellular space extracellular membrane-bounded organelle transport vesicle transport vesicle membrane coated vesicle membrane COPII-coated ER to Golgi transport vesicle ER to Golgi transport vesicle membrane coated vesicle organelle subcompartment endoplasmic reticulum subcompartment nuclear outer membrane-endoplasmic reticulum membrane network endoplasmic reticulum endoplasmic reticulum membrane

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, C	IPR038700	Thiol-activated cytolysin, C-terminal domain superfamily	Homologous Superfamily
A, C	IPR036359	Thiol-activated cytolysin superfamily	Homologous Superfamily
A, C	IPR035390	Thiol-activated cytolysin C-terminal	Domain
A, C	IPR001869	Thiol-activated cytolysin	Family
A, C	IPR036363	Thiol-activated cytolysin, alpha-beta domain superfamily	Homologous Superfamily
B, D	IPR045860	Snake toxin-like superfamily	Homologous Superfamily
B, D	IPR016054	Ly-6 antigen/uPA receptor-like	Domain
B, D	IPR018363	CD59 antigen, conserved site	Conserved Site

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
B, D	Pharos: P13987	primary CD59 deficiency familial hemolytic anemia psoriasis acute myeloid leukemia congenital anemia esophageal adenocarcinoma hemolytic anemia malignant mesothelioma ovarian cancer spina bifida breast cancer Cytopenia large cell medulloblastoma medulloblastoma pilocytic astrocytoma primary CD59 deficiency familial hemolytic anemia psoriasis acute myeloid leukemia congenital anemia esophageal adenocarcinoma hemolytic anemia malignant mesothelioma ovarian cancer spina bifida breast cancer Cytopenia large cell medulloblastoma medulloblastoma pilocytic astrocytoma proteinuria breast carcinoma Down syndrome glioblastoma lung cancer osteosarcoma plasma cell myeloma

Membrane Protein Annotation: OPM OPM Database Homepage

Chains	External Link	Type	Class	Superfamily	Family
A, B, C, D	OPM	Monotopic/peripheral	All beta monotopic/peripheral	Cholesterol-dependent cytolysin	Thiol-activated cytolysin

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.