5VMM | pdb_00005vmm

Staphylococcus aureus IsdB bound to human hemoglobin

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

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
F	SCOP2B Superfamily	NEAT domain-like	8085275	3002054	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	NEAT domain-like	8085275	3002054	SCOP2B (2022-06-29)
H [auth J]	SCOP2 Family	NEAT domain	8085274	4007541	SCOP2 (2022-06-29)
H [auth J]	SCOP2 Superfamily	NEAT domain-like	8085275	3002054	SCOP2 (2022-06-29)
G [auth H]	SCOP2B Superfamily	NEAT domain-like	8085275	3002054	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Globin-like	8039838	3000554	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Globin-like	8039838	3000554	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Globin-like	8039836	3000554	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Globin-like	8039836	3000554	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)
F	NEAT	e5vmmF2	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: NEAT	ECOD (1.6)
F	IsdH_HarA	e5vmmF1	A: alpha arrays	X: Iron-regulated surface determinant protein H linker domain (From Topology)	H: Iron-regulated surface determinant protein H linker domain (From Topology)	T: Iron-regulated surface determinant protein H linker domain	F: IsdH_HarA	ECOD (1.6)
E	NEAT	e5vmmE2	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: NEAT	ECOD (1.6)
E	IsdH_HarA	e5vmmE3	A: alpha arrays	X: Iron-regulated surface determinant protein H linker domain (From Topology)	H: Iron-regulated surface determinant protein H linker domain (From Topology)	T: Iron-regulated surface determinant protein H linker domain	F: IsdH_HarA	ECOD (1.6)
H [auth J]	NEAT	e5vmmJ1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: NEAT	ECOD (1.6)
G [auth H]	NEAT	e5vmmH1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: NEAT	ECOD (1.6)
D	Globin	e5vmmD1	A: alpha arrays	X: Globin-like (From Topology)	H: Globin-like (From Topology)	T: Globin-like	F: Globin	ECOD (1.6)
B	Globin	e5vmmB1	A: alpha arrays	X: Globin-like (From Topology)	H: Globin-like (From Topology)	T: Globin-like	F: Globin	ECOD (1.6)
C	Globin	e5vmmC1	A: alpha arrays	X: Globin-like (From Topology)	H: Globin-like (From Topology)	T: Globin-like	F: Globin	ECOD (1.6)
A	Globin	e5vmmA1	A: alpha arrays	X: Globin-like (From Topology)	H: Globin-like (From Topology)	T: Globin-like	F: Globin	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
E	2.60.40.1850	Mainly Beta	Sandwich	Immunoglobulin-like		CATH (utative)
H [auth J]	2.60.40.1850	Mainly Beta	Sandwich	Immunoglobulin-like		CATH (4.3.0)
G [auth H]	2.60.40.1850	Mainly Beta	Sandwich	Immunoglobulin-like		CATH (4.3.0)
D	1.10.490.10	Mainly Alpha	Orthogonal Bundle	Globin-like	Globins	CATH (4.3.0)
B	1.10.490.10	Mainly Alpha	Orthogonal Bundle	Globin-like	Globins	CATH (4.3.0)
C	1.10.490.10	Mainly Alpha	Orthogonal Bundle	Globin-like	Globins	CATH (4.3.0)
A	1.10.490.10	Mainly Alpha	Orthogonal Bundle	Globin-like	Globins	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
E, F	PF05031	Iron Transport-associated domain (NEAT)	Iron Transport-associated domain	NEAT domains are heme and/or hemoprotein-binding modules highly conserved in secondary structure [1]. They have roles in hemoprotein binding, heme extraction and heme transfer [2]	Domain
E, F	PF20861	Iron-regulated surface determinant protein H/B, linker domain (Isd_H_B_linker)	Iron-regulated surface determinant protein H/B, linker domain	The bacterial pathogen Staphylococcus aureus uses two closely related receptors located on its surface, IsdH and IsdB, to capture from haemoglobin (Hb) the iron it needs to grow. Both proteins show conserved near iron transporter (NEAT) domains (Pfam ...	The bacterial pathogen Staphylococcus aureus uses two closely related receptors located on its surface, IsdH and IsdB, to capture from haemoglobin (Hb) the iron it needs to grow. Both proteins show conserved near iron transporter (NEAT) domains (Pfam:PF05031) that function synergistically. These domains, essential for the arrest of iron, are appropriately positioned by an alpha-helical linker domain (this entry), which does not interact itself with the heme group. In IsdH, this linker domain forms a three-helix bundle structure that is essential for efficient heme capture [1-4].	Domain
G [auth H], H [auth J]	PF05031	Iron Transport-associated domain (NEAT)	Iron Transport-associated domain	NEAT domains are heme and/or hemoprotein-binding modules highly conserved in secondary structure [1]. They have roles in hemoprotein binding, heme extraction and heme transfer [2]	Domain
B, D	PF00042	Globin (Globin)	Globin		Domain
A, C	PF00042	Globin (Globin)	Globin		Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
E, F	Iron-regulated cell wall-anchored protein	heme transmembrane transporter activity transporter activity transmembrane transporter activity cation binding ion binding binding metal ion binding small molecule binding	-	cellular anatomical structure extracellular region
G [auth H], H [auth J]	Iron-regulated cell wall-anchored protein	heme transmembrane transporter activity transporter activity transmembrane transporter activity cation binding ion binding binding metal ion binding small molecule binding	-	cellular anatomical structure extracellular region
B, D	Hemoglobin subunit beta	hemoglobin binding protein binding binding oxygen binding small molecule binding hemoglobin alpha binding oxygen carrier activity molecular carrier activity tetrapyrrole binding heme binding cation binding ion binding metal ion binding	regulation of biosynthetic process regulation of nitric oxide biosynthetic process regulation of biological process regulation of cellular process biological regulation positive regulation of biological process reactive nitrogen species metabolic process nitric oxide metabolic process positive regulation of metabolic process nitric oxide biosynthetic process biosynthetic process positive regulation of biosynthetic process cellular process metabolic process regulation of biosynthetic process regulation of nitric oxide biosynthetic process regulation of biological process regulation of cellular process biological regulation positive regulation of biological process reactive nitrogen species metabolic process nitric oxide metabolic process positive regulation of metabolic process nitric oxide biosynthetic process biosynthetic process positive regulation of biosynthetic process cellular process metabolic process regulation of nitric oxide metabolic process positive regulation of nitric oxide biosynthetic process regulation of metabolic process positive regulation of cellular process catabolic process hydrogen peroxide metabolic process reactive oxygen species metabolic process hydrogen peroxide catabolic process multicellular organismal process system process circulatory system process regulation of blood pressure regulation of biological quality blood circulation regulation of body fluid levels wound healing response to stimulus homotypic cell-cell adhesion cell activation hemostasis platelet aggregation blood coagulation cell adhesion cell-cell adhesion response to stress coagulation response to wounding platelet activation oxygen transport localization transport gas transport establishment of localization one-carbon compound transport carbon dioxide transport renal system process renal absorption nitric oxide transport nitrogen compound transport defense response inflammatory response regulation of tube diameter regulation of tube size vascular process in circulatory system blood vessel diameter maintenance regulation of anatomical structure size response to hydrogen peroxide response to oxidative stress response to chemical response to oxygen-containing compound response to reactive oxygen species cellular response to stimulus cellular detoxification cellular response to chemical stimulus detoxification cellular oxidant detoxification cellular response to toxic substance response to toxic substance	protein-containing complex cellular anatomical structure intracellular anatomical structure hemoglobin complex cytoplasm cytosol haptoglobin-hemoglobin complex extracellular exosome membrane-bounded organelle extracellular vesicle extracellular organelle extracellular region organelle extracellular space protein-containing complex cellular anatomical structure intracellular anatomical structure hemoglobin complex cytoplasm cytosol haptoglobin-hemoglobin complex extracellular exosome membrane-bounded organelle extracellular vesicle extracellular organelle extracellular region organelle extracellular space vesicle extracellular membrane-bounded organelle membrane-enclosed lumen intracellular vesicle ficolin-1-rich granule intracellular membrane-bounded organelle endomembrane system intracellular organelle lumen intracellular organelle organelle lumen cytoplasmic vesicle ficolin-1-rich granule lumen secretory granule secretory vesicle blood microparticle tertiary granule lumen tertiary granule endocytic vesicle lumen endocytic vesicle
A, C	Hemoglobin subunit alpha	oxygen binding binding small molecule binding oxygen carrier activity molecular carrier activity tetrapyrrole binding heme binding cation binding transition metal ion binding iron ion binding ion binding metal ion binding	catabolic process hydrogen peroxide metabolic process reactive oxygen species metabolic process metabolic process cellular process hydrogen peroxide catabolic process oxygen transport localization transport gas transport establishment of localization one-carbon compound transport carbon dioxide transport nitric oxide transport catabolic process hydrogen peroxide metabolic process reactive oxygen species metabolic process metabolic process cellular process hydrogen peroxide catabolic process oxygen transport localization transport gas transport establishment of localization one-carbon compound transport carbon dioxide transport nitric oxide transport nitrogen compound transport response to stimulus defense response response to stress inflammatory response response to hydrogen peroxide response to oxidative stress response to chemical response to oxygen-containing compound response to reactive oxygen species cellular response to stimulus cellular detoxification cellular response to chemical stimulus detoxification cellular oxidant detoxification cellular response to toxic substance response to toxic substance	protein-containing complex cellular anatomical structure intracellular anatomical structure hemoglobin complex cytoplasm cytosol haptoglobin-hemoglobin complex membrane extracellular exosome membrane-bounded organelle extracellular vesicle extracellular organelle extracellular region organelle protein-containing complex cellular anatomical structure intracellular anatomical structure hemoglobin complex cytoplasm cytosol haptoglobin-hemoglobin complex membrane extracellular exosome membrane-bounded organelle extracellular vesicle extracellular organelle extracellular region organelle extracellular space vesicle extracellular membrane-bounded organelle blood microparticle intracellular vesicle membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen intracellular organelle cytoplasmic vesicle organelle lumen endocytic vesicle lumen endocytic vesicle

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
E, F	IPR005877	YSIRK Gram-positive signal peptide	Domain
E, F	IPR050436	Iron-regulated surface determinant protein A	Family
E, F	IPR006635	NEAT domain	Domain
E, F	IPR048652	Iron-regulated surface determinant protein H/B, linker domain	Domain
E, F	IPR019929	Iron-regulated surface determinant protein IsdB	Family
E, F	IPR037250	NEAT domain superfamily	Homologous Superfamily
E, F	IPR019931	LPXTG cell wall anchor domain	Domain
G [auth H], H [auth J]	IPR005877	YSIRK Gram-positive signal peptide	Domain
G [auth H], H [auth J]	IPR050436	Iron-regulated surface determinant protein A	Family
G [auth H], H [auth J]	IPR006635	NEAT domain	Domain
G [auth H], H [auth J]	IPR048652	Iron-regulated surface determinant protein H/B, linker domain	Domain
G [auth H], H [auth J]	IPR019929	Iron-regulated surface determinant protein IsdB	Family
G [auth H], H [auth J]	IPR037250	NEAT domain superfamily	Homologous Superfamily
G [auth H], H [auth J]	IPR019931	LPXTG cell wall anchor domain	Domain
B, D	IPR009050	Globin-like superfamily	Homologous Superfamily
B, D	IPR012292	Globin/Protoglobin	Homologous Superfamily
B, D	IPR000971	Globin	Domain
B, D	IPR050056	Hemoglobin and related oxygen transporters	Family
B, D	IPR002337	Hemoglobin, beta-type	Family
A, C	IPR002338	Hemoglobin, alpha-type	Family
A, C	IPR002339	Hemoglobin, pi	Family
A, C	IPR009050	Globin-like superfamily	Homologous Superfamily
A, C	IPR012292	Globin/Protoglobin	Homologous Superfamily
A, C	IPR000971	Globin	Domain
A, C	IPR050056	Hemoglobin and related oxygen transporters	Family

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
B, D	Pharos: P68871	sickle cell anemia beta thalassemia dominant beta-thalassemia Heinz body anemia polycythemia methemoglobinemia alpha thalassemia echinococcosis acquired polycythemia vera malaria hemoglobin C disease Plasmodium falciparum malaria Cyanosis hemoglobin D disease congenital dyserythropoietic anemia sickle cell anemia beta thalassemia dominant beta-thalassemia Heinz body anemia polycythemia methemoglobinemia alpha thalassemia echinococcosis acquired polycythemia vera malaria hemoglobin C disease Plasmodium falciparum malaria Cyanosis hemoglobin D disease congenital dyserythropoietic anemia inherited hemoglobinopathy familial hemolytic anemia beta-thalassemia HBB/LCRB hemoglobin E disease hemoglobin E-beta-thalassemia syndrome juvenile dermatomyositis delta-beta-thalassemia lung adenocarcinoma lymphoplasmacytic lymphoma malignant ependymoma MALT lymphoma gastric cancer myopathy anemia atypical teratoid rhabdoid tumor pancreatic ductal adenocarcinoma pancreatic intraductal papillary-mucinous neoplasm with low grade dysplasia beta-thalassemia major hemoglobin M disease cerebrovascular disorder hereditary persistence of fetal hemoglobin sickle cell-hemoglobin E disease syndrome thalassemia minor large cell medulloblastoma diabetes mellitus lung cancer Duchenne muscular dystrophy malignant glioma medulloblastoma acute myeloid leukemia gastric carcinoma non-small cell lung carcinoma B-cell chronic lymphocytic leukemia pancreatic intraductal papillary-mucinous carcinoma periodontitis breast cancer hemolytic anemia hereditary persistence of fetal hemoglobin-beta-thalassemia syndrome sickle cell-hemoglobin c disease syndrome thalassemia invasive ductal breast carcinoma tuberculosis limb-girdle muscular dystrophy lung carcinoma ductal breast carcinoma in situ malignant colon neoplasm exocrine pancreatic carcinoma malignant pancreatic neoplasm familial polycythemia atopic eczema head and neck cancer ovarian cancer hemoglobin C-beta-thalassemia syndrome pancreatic intraductal papillary-mucinous neoplasm beta-thalassemia intermedia breast carcinoma hepatocellular carcinoma congenital anemia hypophosphatemic bone disease sickle cell-hemoglobin d disease syndrome
A, C	Pharos: P69905	alpha thalassemia Heinz body anemia acquired polycythemia vera methemoglobinemia hemoglobin H disease polycythemia familial hemolytic anemia alpha thalassemia-intellectual disability syndrome type 1 carcinoma sarcomatoid carcinoma Mammary Neoplasms, Experimental type 2 diabetes mellitus cerebral infarction hemolytic anemia inborn carbohydrate metabolic disorder alpha thalassemia Heinz body anemia acquired polycythemia vera methemoglobinemia hemoglobin H disease polycythemia familial hemolytic anemia alpha thalassemia-intellectual disability syndrome type 1 carcinoma sarcomatoid carcinoma Mammary Neoplasms, Experimental type 2 diabetes mellitus cerebral infarction hemolytic anemia inborn carbohydrate metabolic disorder mammary neoplasms, animal thalassemia congenital anemia facioscapulohumeral muscular dystrophy familial polycythemia hydrops fetalis lung adenocarcinoma beta thalassemia sickle cell anemia Hb Bart's hydrops fetalis hemoglobin M disease maturity-onset diabetes of the young breast carcinoma undifferentiated carcinoma diabetes mellitus