2D5H

Crystal Structure of Recombinant Soybean Proglycinin A3B4 subunit, its Comparison with Mature Glycinin A3B4 subunit, Responsible for Hexamer Assembly

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Protein Modification Annotation

Domain Annotation: SCOP/SCOPe Classification SCOP-e Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A	d2d5ha1	All beta proteins	Double-stranded beta-helix	RmlC-like cupins	automated matches	automated matches	soybean (Glycine max ) [TaxId: 3847 ],	SCOPe (2.08)
B	d2d5hb1	All beta proteins	Double-stranded beta-helix	RmlC-like cupins	automated matches	automated matches	soybean (Glycine max ) [TaxId: 3847 ],	SCOPe (2.08)
C	d2d5hc1	All beta proteins	Double-stranded beta-helix	RmlC-like cupins	automated matches	automated matches	soybean (Glycine max ) [TaxId: 3847 ],	SCOPe (2.08)
D	d2d5hd1	All beta proteins	Double-stranded beta-helix	RmlC-like cupins	automated matches	automated matches	soybean (Glycine max ) [TaxId: 3847 ],	SCOPe (2.08)
E	d2d5he1	All beta proteins	Double-stranded beta-helix	RmlC-like cupins	automated matches	automated matches	soybean (Glycine max ) [TaxId: 3847 ],	SCOPe (2.08)
F	d2d5hf1	All beta proteins	Double-stranded beta-helix	RmlC-like cupins	automated matches	automated matches	soybean (Glycine max ) [TaxId: 3847 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	RmlC-like cupins	8033964	3001825	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	RmlC-like cupins	8033963	3001825	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	RmlC-like cupins	8033963	3001825	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	RmlC-like cupins	8033964	3001825	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	RmlC-like cupins	8033963	3001825	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	RmlC-like cupins	8033964	3001825	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	RmlC-like cupins	8033963	3001825	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	RmlC-like cupins	8033964	3001825	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	RmlC-like cupins	8033964	3001825	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	RmlC-like cupins	8033963	3001825	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	RmlC-like cupins	8033964	3001825	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	RmlC-like cupins	8033963	3001825	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	Cupin_1	e2d5hA3	A: beta sandwiches	X: jelly-roll	H: Double-stranded beta-helix (From Topology)	T: Double-stranded beta-helix	F: Cupin_1	ECOD (1.6)
B	Cupin_1	e2d5hB3	A: beta sandwiches	X: jelly-roll	H: Double-stranded beta-helix (From Topology)	T: Double-stranded beta-helix	F: Cupin_1	ECOD (1.6)
C	Cupin_1	e2d5hC3	A: beta sandwiches	X: jelly-roll	H: Double-stranded beta-helix (From Topology)	T: Double-stranded beta-helix	F: Cupin_1	ECOD (1.6)
D	Cupin_1	e2d5hD1	A: beta sandwiches	X: jelly-roll	H: Double-stranded beta-helix (From Topology)	T: Double-stranded beta-helix	F: Cupin_1	ECOD (1.6)
E	Cupin_1	e2d5hE5	A: beta sandwiches	X: jelly-roll	H: Double-stranded beta-helix (From Topology)	T: Double-stranded beta-helix	F: Cupin_1	ECOD (1.6)
F	Cupin_1	e2d5hF5	A: beta sandwiches	X: jelly-roll	H: Double-stranded beta-helix (From Topology)	T: Double-stranded beta-helix	F: Cupin_1	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	2.60.120.10	Mainly Beta	Sandwich	Jelly Rolls	Jelly Rolls	CATH (4.3.0)
B	2.60.120.10	Mainly Beta	Sandwich	Jelly Rolls	Jelly Rolls	CATH (4.3.0)
C	2.60.120.10	Mainly Beta	Sandwich	Jelly Rolls	Jelly Rolls	CATH (4.3.0)
D	2.60.120.10	Mainly Beta	Sandwich	Jelly Rolls	Jelly Rolls	CATH (4.3.0)
E	2.60.120.10	Mainly Beta	Sandwich	Jelly Rolls	Jelly Rolls	CATH (4.3.0)
F	2.60.120.10	Mainly Beta	Sandwich	Jelly Rolls	Jelly Rolls	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D, E A, B, C, D, E, F	PF00190	Cupin (Cupin_1)	Cupin	This family represents the conserved barrel domain of the 'cupin' superfamily [1] ('cupa' is the Latin term for a small barrel). This family contains 11S and 7S plant seed storage proteins, and germins. Plant seed storage proteins provide the major ...	This family represents the conserved barrel domain of the 'cupin' superfamily [1] ('cupa' is the Latin term for a small barrel). This family contains 11S and 7S plant seed storage proteins, and germins. Plant seed storage proteins provide the major nitrogen source for the developing plant.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D, E A, B, C, D, E, F	glycinin A3B4 subunit	nutrient reservoir activity	-	membrane-bounded organelle storage vacuole intracellular anatomical structure vacuole cellular anatomical entity intracellular membrane-bounded organelle protein storage vacuole intracellular organelle organelle plant-type vacuole cytoplasm aleurone grain intracellular vesicle cytoplasmic vesicle membrane-bounded organelle storage vacuole intracellular anatomical structure vacuole cellular anatomical entity intracellular membrane-bounded organelle protein storage vacuole intracellular organelle organelle plant-type vacuole cytoplasm aleurone grain intracellular vesicle cytoplasmic vesicle vesicle endoplasmic reticulum endomembrane system

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D, E A, B, C, D, E, F	IPR006044	11-S seed storage protein, plant	Family
A, B, C, D, E A, B, C, D, E, F	IPR022379	11-S seed storage protein, conserved site	Conserved Site
A, B, C, D, E A, B, C, D, E, F	IPR006045	Cupin 1	Domain
A, B, C, D, E A, B, C, D, E, F	IPR011051	RmlC-like cupin domain superfamily	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F	IPR050253	Seed Storage and Functional Proteins	Family
A, B, C, D, E A, B, C, D, E, F	IPR014710	RmlC-like jelly roll fold	Homologous Superfamily

Protein Modification Annotation

Modified Residue(s)
Chain	Residue(s)	Description
A, B, C, D, E A, B, C, D, E, F	CSD	Parent Component: CYS RESID: AA0262 PSI-MOD : L-cysteine sulfinic acid MOD:00267

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.