1QDM | pdb_00001qdm

CRYSTAL STRUCTURE OF PROPHYTEPSIN, A ZYMOGEN OF A BARLEY VACUOLAR ASPARTIC PROTEINASE.

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 Classification
Domain Annotation: CATH
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Membrane Protein Annotation: OPM

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

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
C	d1qdmc1	All alpha proteins	Saposin-like	Saposin	Swaposin	(Pro)phytepsin	(Hordeum vulgare ) [TaxId: 4513 ],	SCOPe (2.08)
C	d1qdmc2	All beta proteins	Acid proteases	Acid proteases	Pepsin-like	Plant acid proteinase, phytepsin	(Hordeum vulgare ) [TaxId: 4513 ],	SCOPe (2.08)
B	d1qdmb1	All alpha proteins	Saposin-like	Saposin	Swaposin	(Pro)phytepsin	(Hordeum vulgare ) [TaxId: 4513 ],	SCOPe (2.08)
B	d1qdmb2	All beta proteins	Acid proteases	Acid proteases	Pepsin-like	Plant acid proteinase, phytepsin	(Hordeum vulgare ) [TaxId: 4513 ],	SCOPe (2.08)
A	d1qdma1	All alpha proteins	Saposin-like	Saposin	Swaposin	(Pro)phytepsin	(Hordeum vulgare ) [TaxId: 4513 ],	SCOPe (2.08)
A	d1qdma2	All beta proteins	Acid proteases	Acid proteases	Pepsin-like	Plant acid proteinase, phytepsin	(Hordeum vulgare ) [TaxId: 4513 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
C	SCOP2B Superfamily	Acid proteases	8042471	3001059	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Acid proteases	8042471	3001059	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Acid proteases	8042471	3001059	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Acid proteases	8042471	3001059	SCOP2B (2022-06-29)
A	SCOP2 Family	Swaposin	8025399	4001057	SCOP2 (2022-06-29)
A	SCOP2 Family	Pepsin-like	8030092	4002301	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Saposin	8037778	3000601	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Acid proteases	8042471	3001059	SCOP2 (2022-06-29)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
C	2.40.70.10	Mainly Beta	Beta Barrel	Cathepsin D, subunit A	domain 1	CATH (4.3.0)
C	1.10.225.10	Mainly Alpha	Orthogonal Bundle	NK-Lysin	Saposin-like	CATH (4.3.0)
B	2.40.70.10	Mainly Beta	Beta Barrel	Cathepsin D, subunit A	domain 1	CATH (4.3.0)
B	1.10.225.10	Mainly Alpha	Orthogonal Bundle	NK-Lysin	Saposin-like	CATH (4.3.0)
A	2.40.70.10	Mainly Beta	Beta Barrel	Cathepsin D, subunit A	domain 1	CATH (4.3.0)
A	1.10.225.10	Mainly Alpha	Orthogonal Bundle	NK-Lysin	Saposin-like	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C	PF05184	Saposin-like type B, region 1 (SapB_1)	Saposin-like type B, region 1	Saposin B is a small non-enzymatic glycoprotein required for the breakdown of cerebroside sulphates (sulphatides) in lysosomes. Saposin B contains three intramolecular disulphide bridges, exists as a dimer and is remarkably heat, protease, and pH sta ...	Saposin B is a small non-enzymatic glycoprotein required for the breakdown of cerebroside sulphates (sulphatides) in lysosomes. Saposin B contains three intramolecular disulphide bridges, exists as a dimer and is remarkably heat, protease, and pH stable. The crystal structure of human saposin B reveals an unusual shell-like dimer consisting of a monolayer of alpha-helices enclosing a large hydrophobic cavity [1,2]. It is one of the most studied members of the saposin protein family and it is involved in the hydrolysis of glycolipids and glycerolipids. SapB is unique in the saposin family in that it facilitates degradation by interacting with the substrate, not the enzymes [3].	Domain
A, B, C	PF03489	Saposin-like type B, region 2 (SapB_2)	Saposin-like type B, region 2	-	Family
A, B, C	PF00026	Eukaryotic aspartyl protease (Asp)	Eukaryotic aspartyl protease	Aspartyl (acid) proteases include pepsins, cathepsins, and renins. Two-domain structure, probably arising from ancestral duplication. This family does not include the retroviral nor retrotransposon proteases (Pfam:PF00077), which are much smaller a ...	Aspartyl (acid) proteases include pepsins, cathepsins, and renins. Two-domain structure, probably arising from ancestral duplication. This family does not include the retroviral nor retrotransposon proteases (Pfam:PF00077), which are much smaller and appear to be homologous to a single domain of the eukaryotic asp proteases.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C	PROPHYTEPSIN	aspartic-type peptidase activity peptidase activity catalytic activity, acting on a protein hydrolase activity aspartic-type endopeptidase activity catalytic activity endopeptidase activity	primary metabolic process metabolic process cellular process lipid metabolic process proteolysis protein metabolic process macromolecule metabolic process	membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure organelle vacuole cytoplasm intracellular membrane-bounded organelle

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C	IPR033869	Phytepsin	Domain
A, B, C	IPR011001	Saposin-like	Homologous Superfamily
A, B, C	IPR007856	Saposin-like type B, region 1	Domain
A, B, C	IPR008139	Saposin B type domain	Domain
A, B, C	IPR001461	Aspartic peptidase A1	Family
A, B, C	IPR033121	Peptidase family A1 domain	Domain
A, B, C	IPR008138	Saposin B type, region 2	Domain
A, B, C	IPR021109	Aspartic peptidase domain superfamily	Homologous Superfamily
A, B, C	IPR001969	Aspartic peptidase, active site	Active Site

Membrane Protein Annotation: OPM OPM Database Homepage

Chains	External Link	Type	Class	Superfamily	Family
A, B, C	OPM	Monotopic/peripheral	All beta monotopic/peripheral	Peptidase clan AA	Eukaryotic aspartyl protease

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.