5M3L | pdb_00005m3l

Single-particle cryo-EM using alignment by classification (ABC): the structure of Lumbricus terrestris 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

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
O	SCOP2B Superfamily	LDL receptor-like module	8042065	3000728	SCOP2B (2022-06-29)
O	SCOP2B Superfamily	Heterotrimerisation domain of extracellular hemoglobin linker subunits	8042067	3000575	SCOP2B (2022-06-29)
O	SCOP2B Superfamily	Extracellular hemoglobin linker subunit, receptor domain	8042064	3000638	SCOP2B (2022-06-29)
N	SCOP2B Superfamily	Extracellular hemoglobin linker subunit, receptor domain	8042059	3000638	SCOP2B (2022-06-29)
N	SCOP2B Superfamily	LDL receptor-like module	8042061	3000728	SCOP2B (2022-06-29)
N	SCOP2B Superfamily	Heterotrimerisation domain of extracellular hemoglobin linker subunits	8042063	3000575	SCOP2B (2022-06-29)
M	SCOP2B Superfamily	Extracellular hemoglobin linker subunit, receptor domain	8042055	3000638	SCOP2B (2022-06-29)
M	SCOP2B Superfamily	LDL receptor-like module	8042056	3000728	SCOP2B (2022-06-29)
M	SCOP2B Superfamily	Heterotrimerisation domain of extracellular hemoglobin linker subunits	8042058	3000575	SCOP2B (2022-06-29)
L	SCOP2B Superfamily	Globin-like	8043790	3000554	SCOP2B (2022-06-29)
H	SCOP2B Superfamily	Globin-like	8043790	3000554	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Globin-like	8043790	3000554	SCOP2B (2022-06-29)
K	SCOP2B Superfamily	Globin-like	8043789	3000554	SCOP2B (2022-06-29)
G	SCOP2B Superfamily	Globin-like	8043789	3000554	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Globin-like	8043789	3000554	SCOP2B (2022-06-29)
J	SCOP2B Superfamily	Globin-like	8043788	3000554	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	Globin-like	8043788	3000554	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Globin-like	8043788	3000554	SCOP2B (2022-06-29)
I	SCOP2B Superfamily	Globin-like	8043787	3000554	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	Globin-like	8043787	3000554	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Globin-like	8043787	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)
M	Eryth_link_C_1	e5m3lM2	A: beta barrels	X: Lipocalins/Streptavidin	H: Quinohemoprotein amine dehydrogenase A chain, domain 3-like (From Topology)	T: Quinohemoprotein amine dehydrogenase A chain, domain 3-like	F: Eryth_link_C_1	ECOD (1.6)
M	Ldl_recept_a	e5m3lM3	A: few secondary structure elements	X: EGF-like	H: LDL receptor-like module (From Topology)	T: LDL receptor-like module	F: Ldl_recept_a	ECOD (1.6)
M	EUF08728	e5m3lM1	A: few secondary structure elements	X: EGF-like	H: LDL receptor-like module (From Topology)	T: LDL receptor-like module	F: EUF08728	ECOD (1.6)
L	Globin	e5m3lL1	A: alpha arrays	X: Globin-like (From Topology)	H: Globin-like (From Topology)	T: Globin-like	F: Globin	ECOD (1.6)
H	Globin	e5m3lH1	A: alpha arrays	X: Globin-like (From Topology)	H: Globin-like (From Topology)	T: Globin-like	F: Globin	ECOD (1.6)
D	Globin	e5m3lD1	A: alpha arrays	X: Globin-like (From Topology)	H: Globin-like (From Topology)	T: Globin-like	F: Globin	ECOD (1.6)
K	Globin	e5m3lK1	A: alpha arrays	X: Globin-like (From Topology)	H: Globin-like (From Topology)	T: Globin-like	F: Globin	ECOD (1.6)
G	Globin	e5m3lG1	A: alpha arrays	X: Globin-like (From Topology)	H: Globin-like (From Topology)	T: Globin-like	F: Globin	ECOD (1.6)
C	Globin	e5m3lC1	A: alpha arrays	X: Globin-like (From Topology)	H: Globin-like (From Topology)	T: Globin-like	F: Globin	ECOD (1.6)
J	Globin	e5m3lJ1	A: alpha arrays	X: Globin-like (From Topology)	H: Globin-like (From Topology)	T: Globin-like	F: Globin	ECOD (1.6)
F	Globin	e5m3lF1	A: alpha arrays	X: Globin-like (From Topology)	H: Globin-like (From Topology)	T: Globin-like	F: Globin	ECOD (1.6)
B	Globin	e5m3lB1	A: alpha arrays	X: Globin-like (From Topology)	H: Globin-like (From Topology)	T: Globin-like	F: Globin	ECOD (1.6)
I	Globin	e5m3lI1	A: alpha arrays	X: Globin-like (From Topology)	H: Globin-like (From Topology)	T: Globin-like	F: Globin	ECOD (1.6)
E	Globin	e5m3lE1	A: alpha arrays	X: Globin-like (From Topology)	H: Globin-like (From Topology)	T: Globin-like	F: Globin	ECOD (1.6)
A	Globin	e5m3lA1	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)
O	6.10.250.1540	Special	Helix non-globular	Single alpha-helices involved in coiled-coils or other helix-helix interfaces		CATH (utative)
O	2.40.128.620	Mainly Beta	Beta Barrel	Lipocalin		CATH (utative)
N	6.10.250.1530	Special	Helix non-globular	Single alpha-helices involved in coiled-coils or other helix-helix interfaces		CATH (utative)
N	2.40.128.620	Mainly Beta	Beta Barrel	Lipocalin		CATH (utative)
M	6.10.250.1520	Special	Helix non-globular	Single alpha-helices involved in coiled-coils or other helix-helix interfaces		CATH (utative)
M	2.40.128.620	Mainly Beta	Beta Barrel	Lipocalin		CATH (utative)
L	1.10.490.10	Mainly Alpha	Orthogonal Bundle	Globin-like	Globins	CATH (utative)
H	1.10.490.10	Mainly Alpha	Orthogonal Bundle	Globin-like	Globins	CATH (utative)
D	1.10.490.10	Mainly Alpha	Orthogonal Bundle	Globin-like	Globins	CATH (utative)
K	1.10.490.10	Mainly Alpha	Orthogonal Bundle	Globin-like	Globins	CATH (utative)
G	1.10.490.10	Mainly Alpha	Orthogonal Bundle	Globin-like	Globins	CATH (utative)
C	1.10.490.10	Mainly Alpha	Orthogonal Bundle	Globin-like	Globins	CATH (utative)
J	1.10.490.10	Mainly Alpha	Orthogonal Bundle	Globin-like	Globins	CATH (utative)
F	1.10.490.10	Mainly Alpha	Orthogonal Bundle	Globin-like	Globins	CATH (utative)
B	1.10.490.10	Mainly Alpha	Orthogonal Bundle	Globin-like	Globins	CATH (utative)
I	1.10.490.10	Mainly Alpha	Orthogonal Bundle	Globin-like	Globins	CATH (utative)
E	1.10.490.10	Mainly Alpha	Orthogonal Bundle	Globin-like	Globins	CATH (utative)
A	1.10.490.10	Mainly Alpha	Orthogonal Bundle	Globin-like	Globins	CATH (utative)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
O	PF16915	Annelid erythrocruorin linker subunit C-terminus (Eryth_link_C)	Annelid erythrocruorin linker subunit C-terminus	This domain is found in linker subunits of the erythrocruorin respiratory complex in annelid worms [1].	Domain
O	PF00057	Low-density lipoprotein receptor domain class A (Ldl_recept_a)	Low-density lipoprotein receptor domain class A	-	Repeat
N	PF16915	Annelid erythrocruorin linker subunit C-terminus (Eryth_link_C)	Annelid erythrocruorin linker subunit C-terminus	This domain is found in linker subunits of the erythrocruorin respiratory complex in annelid worms [1].	Domain
N	PF00057	Low-density lipoprotein receptor domain class A (Ldl_recept_a)	Low-density lipoprotein receptor domain class A	-	Repeat
M	PF16915	Annelid erythrocruorin linker subunit C-terminus (Eryth_link_C)	Annelid erythrocruorin linker subunit C-terminus	This domain is found in linker subunits of the erythrocruorin respiratory complex in annelid worms [1].	Domain
M	PF00057	Low-density lipoprotein receptor domain class A (Ldl_recept_a)	Low-density lipoprotein receptor domain class A	-	Repeat
D, H, L	PF00042	Globin (Globin)	Globin		Domain
C, G, K	PF00042	Globin (Globin)	Globin		Domain
B, F, J	PF00042	Globin (Globin)	Globin		Domain
A, E, I	PF00042	Globin (Globin)	Globin		Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
O	Extracellular hemoglobin linker L3 subunit	cation binding ion binding binding metal ion binding small molecule binding	-	-
N	Extracellular hemoglobin linker L2 subunit	cation binding ion binding binding metal ion binding small molecule binding	-	-
M	Hemoglobin linker chain L1	cation binding ion binding binding metal ion binding small molecule binding	-	-
D, H, L	Hemoglobin chain d1	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	-	protein-containing complex cellular anatomical structure intracellular anatomical structure hemoglobin complex cytoplasm cytosol extracellular region
C, G, K	Extracellular globin-3	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	-	protein-containing complex cellular anatomical structure intracellular anatomical structure hemoglobin complex cytoplasm cytosol extracellular region
B, F, J	Extracellular globin-2	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	-	protein-containing complex cellular anatomical structure intracellular anatomical structure hemoglobin complex cytoplasm cytosol extracellular region
A, E, I	Extracellular globin-4	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	-	protein-containing complex cellular anatomical structure intracellular anatomical structure hemoglobin complex cytoplasm cytosol extracellular region

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
O	IPR002172	Low-density lipoprotein (LDL) receptor class A repeat	Repeat
O	IPR023415	Low-density lipoprotein (LDL) receptor class A, conserved site	Conserved Site
O	IPR036055	LDL receptor-like superfamily	Homologous Superfamily
O	IPR031639	Annelid erythrocruorin linker subunit, C-terminal	Domain
O	IPR036153	Erythrocruorin linker subunit, C-terminal superfamily	Homologous Superfamily
O	IPR037246	Extracellular hemoglobin linker subunit, heterodimerisation domain	Homologous Superfamily
N	IPR002172	Low-density lipoprotein (LDL) receptor class A repeat	Repeat
N	IPR023415	Low-density lipoprotein (LDL) receptor class A, conserved site	Conserved Site
N	IPR036055	LDL receptor-like superfamily	Homologous Superfamily
N	IPR031639	Annelid erythrocruorin linker subunit, C-terminal	Domain
N	IPR036153	Erythrocruorin linker subunit, C-terminal superfamily	Homologous Superfamily
N	IPR037246	Extracellular hemoglobin linker subunit, heterodimerisation domain	Homologous Superfamily
M	IPR002172	Low-density lipoprotein (LDL) receptor class A repeat	Repeat
M	IPR023415	Low-density lipoprotein (LDL) receptor class A, conserved site	Conserved Site
M	IPR036055	LDL receptor-like superfamily	Homologous Superfamily
M	IPR031639	Annelid erythrocruorin linker subunit, C-terminal	Domain
M	IPR036153	Erythrocruorin linker subunit, C-terminal superfamily	Homologous Superfamily
M	IPR037246	Extracellular hemoglobin linker subunit, heterodimerisation domain	Homologous Superfamily
D, H, L	IPR044399	Myoglobin-like, M family globin domain	Domain
D, H, L	IPR014610	Globin, extracellular	Family
D, H, L	IPR009050	Globin-like superfamily	Homologous Superfamily
D, H, L	IPR000971	Globin	Domain
D, H, L	IPR012292	Globin/Protoglobin	Homologous Superfamily
C, G, K	IPR044399	Myoglobin-like, M family globin domain	Domain
C, G, K	IPR014610	Globin, extracellular	Family
C, G, K	IPR009050	Globin-like superfamily	Homologous Superfamily
C, G, K	IPR000971	Globin	Domain
C, G, K	IPR012292	Globin/Protoglobin	Homologous Superfamily
B, F, J	IPR044399	Myoglobin-like, M family globin domain	Domain
B, F, J	IPR014610	Globin, extracellular	Family
B, F, J	IPR002336	Erythrocruorin	Family
B, F, J	IPR009050	Globin-like superfamily	Homologous Superfamily
B, F, J	IPR000971	Globin	Domain
B, F, J	IPR012292	Globin/Protoglobin	Homologous Superfamily
A, E, I	IPR044399	Myoglobin-like, M family globin domain	Domain
A, E, I	IPR014610	Globin, extracellular	Family
A, E, I	IPR009050	Globin-like superfamily	Homologous Superfamily
A, E, I	IPR000971	Globin	Domain
A, E, I	IPR012292	Globin/Protoglobin	Homologous Superfamily

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.id_divider{ color: #ccc; padding: 0 10px 0 10px; } .extended_id_info{ color: #ccc; font-size: 18px; position: relative; top: -10px; left: 4px; } 5M3L | pdb_00005m3l

Single-particle cryo-EM using alignment by classification (ABC): the structure of Lumbricus terrestris hemoglobin

External Resource: Annotation

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Domain Annotation: ECOD Classification ECOD Database Homepage

Domain Annotation: CATH CATH Database Homepage

Protein Family Annotation Pfam Database Homepage

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

InterPro: Protein Family Classification InterPro Database Homepage

5M3L | pdb_00005m3l