4YXA | pdb_00004yxa

Complex of SpaO(SPOA1,2 SeMet) and OrgB(APAR)::T4lysozyme fusion protein

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

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
F	SCOP2B Superfamily	Lysozyme-like	8033861	3001879	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Lysozyme-like	8033861	3001879	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	Surface presentation of antigens (SPOA)	8098672	3001883	SCOP2B (2022-06-29)
B	SCOP2 Family	Surface presentation of antigens (SPOA)-like	8098671	4000884	SCOP2 (2022-06-29)
B	SCOP2 Superfamily	Surface presentation of antigens (SPOA)	8098672	3001883	SCOP2 (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
F		e4yxaF1	A: a/b three-layered sandwiches	X: Lipocalins/Streptavidin	H: Fibronectin type I module-like	T: Fibronectin type I module	F:	ECOD (v294.1)
C	PCI	e4yxaC1	A: a/b three-layered sandwiches	X: Lipocalins/Streptavidin	H: Fibronectin type I module-like	T: Fibronectin type I module	F: PCI	ECOD (v294.1)
E		e4yxaE1	A: a/b three-layered sandwiches	X: cradle loop barrel	H: RIFT-related	T: acid protease	F:	ECOD (v294.1)
B	HypA	e4yxaB1	A: a/b three-layered sandwiches	X: Ribosomal protein S7	H: HypA Ni-binding domain	T: HypA Ni-binding domain	F: HypA	ECOD (v294.1)
D	HypA	e4yxaD1	A: a/b three-layered sandwiches	X: Ribosomal protein S7	H: HypA Ni-binding domain	T: HypA Ni-binding domain	F: HypA	ECOD (v294.1)
A	Lactamase_B_2	e4yxaA1	A: a/b three-layered sandwiches	X: Cytidine deaminase-like	H: Cytidine deaminase-like	T: Cytidine deaminase-like	F: Lactamase_B_2	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
F	1.10.530.40	Mainly Alpha	Orthogonal Bundle	Lysozyme		CATH (4.3.0)
C	1.10.530.40	Mainly Alpha	Orthogonal Bundle	Lysozyme		CATH (4.3.0)
E	2.30.330.10	Mainly Beta	Roll	Surface presentation of antigens (SPOA)	SpoA-like	CATH (4.3.0)
B	2.30.330.10	Mainly Beta	Roll	Surface presentation of antigens (SPOA)	SpoA-like	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
C, F	PF00959	Phage lysozyme (Phage_lysozyme)	Phage lysozyme	This family includes lambda phage lysozyme and E. coli endolysin.	Domain
B, E	PF01052	Type III flagellar switch regulator (C-ring) FliN C-term (FliMN_C)	Type III flagellar switch regulator (C-ring) FliN C-term	This family includes the C-terminal region of flagellar motor switch proteins FliN and FliM. It is associated with family FliM, Pfam:PF02154 and family FliN_N Pfam:PF16973.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
C, F	Oxygen-regulated invasion protein OrgB,Endolysin	hydrolase activity, acting on glycosyl bonds peptidoglycan muralytic activity hydrolase activity, hydrolyzing O-glycosyl compounds lysozyme activity hydrolase activity catalytic activity	defense response to bacterium biological process involved in interspecies interaction between organisms response to stimulus response to other organism defense response response to bacterium response to stress response to external stimulus response to external biotic stimulus response to biotic stimulus carbohydrate derivative catabolic process catabolic process peptidoglycan catabolic process glycosaminoglycan metabolic process defense response to bacterium biological process involved in interspecies interaction between organisms response to stimulus response to other organism defense response response to bacterium response to stress response to external stimulus response to external biotic stimulus response to biotic stimulus carbohydrate derivative catabolic process catabolic process peptidoglycan catabolic process glycosaminoglycan metabolic process carbohydrate derivative metabolic process aminoglycan catabolic process macromolecule catabolic process glycosaminoglycan catabolic process aminoglycan metabolic process peptidoglycan metabolic process metabolic process cellular process macromolecule metabolic process symbiont-mediated cytolysis of host cell viral life cycle disruption of cell in another organism cytolysis biological process involved in interaction with host biological process involved in symbiotic interaction viral release from host cell by cytolysis exit from host cell viral process cytolysis in another organism viral release from host cell disruption of anatomical structure in another organism symbiont-mediated killing of host cell killing of cells of another organism cell killing cell wall organization or biogenesis cell wall macromolecule catabolic process cell wall macromolecule metabolic process localization establishment of protein localization protein transport transport macromolecule localization intracellular protein localization establishment of localization	host cellular component host intracellular part cellular anatomical structure host cell cytoplasm host cell part host intracellular region other organism part intracellular anatomical structure cytoplasm
B, E	Surface presentation of antigens protein SpaO	-	positive chemotaxis chemotaxis response to stimulus taxis response to chemical response to external stimulus locomotion bacterial-type flagellum-dependent swarming motility bacterial-type flagellum-dependent cell motility cellular process cell motility archaeal or bacterial-type flagellum-dependent cell motility cilium or flagellum-dependent cell motility establishment of protein localization positive chemotaxis chemotaxis response to stimulus taxis response to chemical response to external stimulus locomotion bacterial-type flagellum-dependent swarming motility bacterial-type flagellum-dependent cell motility cellular process cell motility archaeal or bacterial-type flagellum-dependent cell motility cilium or flagellum-dependent cell motility establishment of protein localization transport secretion protein secretion by the type III secretion system establishment of protein localization to extracellular region export from cell protein secretion establishment of localization protein localization to extracellular region transmembrane transport localization secretion by cell protein transmembrane transport protein transport macromolecule localization intracellular protein localization	-
A, D	Surface presentation of antigens protein SpaO	-	positive chemotaxis chemotaxis response to stimulus taxis response to chemical response to external stimulus locomotion bacterial-type flagellum-dependent swarming motility bacterial-type flagellum-dependent cell motility cellular process cell motility archaeal or bacterial-type flagellum-dependent cell motility cilium or flagellum-dependent cell motility establishment of protein localization positive chemotaxis chemotaxis response to stimulus taxis response to chemical response to external stimulus locomotion bacterial-type flagellum-dependent swarming motility bacterial-type flagellum-dependent cell motility cellular process cell motility archaeal or bacterial-type flagellum-dependent cell motility cilium or flagellum-dependent cell motility establishment of protein localization transport secretion protein secretion by the type III secretion system establishment of protein localization to extracellular region export from cell protein secretion establishment of localization protein localization to extracellular region transmembrane transport localization secretion by cell protein transmembrane transport protein transport macromolecule localization intracellular protein localization	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
C, F	IPR052619	Bacteriophage lysozyme-like	Family
C, F	IPR001165	T4-type lysozyme	Family
C, F	IPR034690	Endolysin T4 type	Family
C, F	IPR002196	Glycoside hydrolase, family 24	Family
C, F	IPR023347	Lysozyme domain superfamily	Homologous Superfamily
C, F	IPR023346	Lysozyme-like domain superfamily	Homologous Superfamily
C, F	IPR058103	SPI-1 type 3 secretion system stator protein	Family
B, E	IPR003283	Type III secretion system outer membrane, SpaO	Family
B, E	IPR058805	SpaO, FliM/N C-terminal related	Domain
B, E	IPR001543	Flagellar motor switch protein FliN-like, C-terminal domain	Domain
B, E	IPR058804	SpaO, N-terminal domain	Domain
B, E	IPR036429	SpoA-like superfamily	Homologous Superfamily
B, E	IPR013385	Type III secretion system apparatus protein YscQ/HrcQ/SpaO	Family
A, D	IPR003283	Type III secretion system outer membrane, SpaO	Family
A, D	IPR058805	SpaO, FliM/N C-terminal related	Domain
A, D	IPR001543	Flagellar motor switch protein FliN-like, C-terminal domain	Domain
A, D	IPR058804	SpaO, N-terminal domain	Domain
A, D	IPR036429	SpoA-like superfamily	Homologous Superfamily
A, D	IPR013385	Type III secretion system apparatus protein YscQ/HrcQ/SpaO	Family

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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.