2GRA

crystal structure of Human Pyrroline-5-carboxylate Reductase complexed with nadp

External Resource: Annotation

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

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A	d2graa2	All alpha proteins	6-phosphogluconate dehydrogenase C-terminal domain-like	6-phosphogluconate dehydrogenase C-terminal domain-like	automated matches	automated matches	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
A	d2graa1	Alpha and beta proteins (a/b)	NAD(P)-binding Rossmann-fold domains	NAD(P)-binding Rossmann-fold domains	automated matches	automated matches	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
A	d2graa3	Artifacts	Tags	Tags	Tags	N-terminal Tags	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
B	d2grab2	All alpha proteins	6-phosphogluconate dehydrogenase C-terminal domain-like	6-phosphogluconate dehydrogenase C-terminal domain-like	automated matches	automated matches	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
B	d2grab1	Alpha and beta proteins (a/b)	NAD(P)-binding Rossmann-fold domains	NAD(P)-binding Rossmann-fold domains	automated matches	automated matches	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
B	d2grab3	Artifacts	Tags	Tags	Tags	N-terminal Tags	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
C	d2grac2	All alpha proteins	6-phosphogluconate dehydrogenase C-terminal domain-like	6-phosphogluconate dehydrogenase C-terminal domain-like	automated matches	automated matches	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
C	d2grac1	Alpha and beta proteins (a/b)	NAD(P)-binding Rossmann-fold domains	NAD(P)-binding Rossmann-fold domains	automated matches	automated matches	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
C	d2grac3	Artifacts	Tags	Tags	Tags	N-terminal Tags	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
D	d2grad2	All alpha proteins	6-phosphogluconate dehydrogenase C-terminal domain-like	6-phosphogluconate dehydrogenase C-terminal domain-like	automated matches	automated matches	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
D	d2grad1	Alpha and beta proteins (a/b)	NAD(P)-binding Rossmann-fold domains	NAD(P)-binding Rossmann-fold domains	automated matches	automated matches	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
D	d2grad3	Artifacts	Tags	Tags	Tags	N-terminal Tags	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
E	d2grae2	All alpha proteins	6-phosphogluconate dehydrogenase C-terminal domain-like	6-phosphogluconate dehydrogenase C-terminal domain-like	automated matches	automated matches	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
E	d2grae1	Alpha and beta proteins (a/b)	NAD(P)-binding Rossmann-fold domains	NAD(P)-binding Rossmann-fold domains	automated matches	automated matches	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
E	d2grae3	Artifacts	Tags	Tags	Tags	N-terminal Tags	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A	P5CR_dimer	e2graA1	A: alpha arrays	X: 6-phosphogluconate dehydrogenase C-terminal domain-like (From Topology)	H: 6-phosphogluconate dehydrogenase C-terminal domain-like (From Topology)	T: 6-phosphogluconate dehydrogenase C-terminal domain-like	F: P5CR_dimer	ECOD (1.6)
A	F420_oxidored	e2graA2	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: NAD(P)-binding Rossmann-fold domains	F: F420_oxidored	ECOD (1.6)
B	P5CR_dimer	e2graB1	A: alpha arrays	X: 6-phosphogluconate dehydrogenase C-terminal domain-like (From Topology)	H: 6-phosphogluconate dehydrogenase C-terminal domain-like (From Topology)	T: 6-phosphogluconate dehydrogenase C-terminal domain-like	F: P5CR_dimer	ECOD (1.6)
B	F420_oxidored	e2graB2	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: NAD(P)-binding Rossmann-fold domains	F: F420_oxidored	ECOD (1.6)
C	P5CR_dimer	e2graC1	A: alpha arrays	X: 6-phosphogluconate dehydrogenase C-terminal domain-like (From Topology)	H: 6-phosphogluconate dehydrogenase C-terminal domain-like (From Topology)	T: 6-phosphogluconate dehydrogenase C-terminal domain-like	F: P5CR_dimer	ECOD (1.6)
C	F420_oxidored	e2graC2	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: NAD(P)-binding Rossmann-fold domains	F: F420_oxidored	ECOD (1.6)
D	P5CR_dimer	e2graD1	A: alpha arrays	X: 6-phosphogluconate dehydrogenase C-terminal domain-like (From Topology)	H: 6-phosphogluconate dehydrogenase C-terminal domain-like (From Topology)	T: 6-phosphogluconate dehydrogenase C-terminal domain-like	F: P5CR_dimer	ECOD (1.6)
D	F420_oxidored	e2graD2	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: NAD(P)-binding Rossmann-fold domains	F: F420_oxidored	ECOD (1.6)
E	P5CR_dimer	e2graE1	A: alpha arrays	X: 6-phosphogluconate dehydrogenase C-terminal domain-like (From Topology)	H: 6-phosphogluconate dehydrogenase C-terminal domain-like (From Topology)	T: 6-phosphogluconate dehydrogenase C-terminal domain-like	F: P5CR_dimer	ECOD (1.6)
E	F420_oxidored	e2graE2	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: NAD(P)-binding Rossmann-fold domains	F: F420_oxidored	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.40.50.720	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	NAD(P)-binding Rossmann-like Domain	CATH (4.3.0)
A	1.10.3730.10	Mainly Alpha	Orthogonal Bundle	ProC C-terminal domain-like fold	ProC C-terminal domain-like	CATH (4.3.0)
B	3.40.50.720	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	NAD(P)-binding Rossmann-like Domain	CATH (4.3.0)
B	1.10.3730.10	Mainly Alpha	Orthogonal Bundle	ProC C-terminal domain-like fold	ProC C-terminal domain-like	CATH (4.3.0)
C	3.40.50.720	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	NAD(P)-binding Rossmann-like Domain	CATH (4.3.0)
C	1.10.3730.10	Mainly Alpha	Orthogonal Bundle	ProC C-terminal domain-like fold	ProC C-terminal domain-like	CATH (4.3.0)
D	3.40.50.720	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	NAD(P)-binding Rossmann-like Domain	CATH (4.3.0)
D	1.10.3730.10	Mainly Alpha	Orthogonal Bundle	ProC C-terminal domain-like fold	ProC C-terminal domain-like	CATH (4.3.0)
E	3.40.50.720	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	NAD(P)-binding Rossmann-like Domain	CATH (4.3.0)
E	1.10.3730.10	Mainly Alpha	Orthogonal Bundle	ProC C-terminal domain-like fold	ProC C-terminal domain-like	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D, E	PF14748	Pyrroline-5-carboxylate reductase dimerisation (P5CR_dimer)	Pyrroline-5-carboxylate reductase dimerisation	Pyrroline-5-carboxylate reductase consists of two domains, an N-terminal catalytic domain (Pfam:PF03807) and a C-terminal dimerisation domain. This is the dimerisation domain [1].	Domain
A, B, C, D, E	PF03807	NADP oxidoreductase coenzyme F420-dependent (F420_oxidored)	NADP oxidoreductase coenzyme F420-dependent	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D, E	Pyrroline-5-carboxylate reductase 1	oxidoreductase activity oxidoreductase activity, acting on the CH-NH group of donors, NAD or NADP as acceptor oxidoreductase activity, acting on the CH-NH group of donors pyrroline-5-carboxylate reductase activity catalytic activity identical protein binding protein binding binding	glutamine family amino acid biosynthetic process oxoacid metabolic process cellular biosynthetic process organonitrogen compound biosynthetic process amino acid metabolic process L-proline biosynthetic process organic acid metabolic process organic acid biosynthetic process alpha-amino acid metabolic process carboxylic acid biosynthetic process glutamine family amino acid metabolic process proline metabolic process organic substance metabolic process organic substance biosynthetic process glutamine family amino acid biosynthetic process oxoacid metabolic process cellular biosynthetic process organonitrogen compound biosynthetic process amino acid metabolic process L-proline biosynthetic process organic acid metabolic process organic acid biosynthetic process alpha-amino acid metabolic process carboxylic acid biosynthetic process glutamine family amino acid metabolic process proline metabolic process organic substance metabolic process organic substance biosynthetic process small molecule metabolic process proline biosynthetic process organonitrogen compound metabolic process small molecule biosynthetic process cellular metabolic process carboxylic acid metabolic process primary metabolic process L-amino acid biosynthetic process L-amino acid metabolic process organic cyclic compound metabolic process proteinogenic amino acid metabolic process amino acid biosynthetic process biosynthetic process organic cyclic compound biosynthetic process proteinogenic amino acid biosynthetic process metabolic process cellular process alpha-amino acid biosynthetic process regulation of mitochondrial membrane potential biological regulation regulation of biological quality regulation of membrane potential cellular response to stimulus intrinsic apoptotic signaling pathway in response to oxidative stress neuron apoptotic process regulation of cellular process regulation of oxidative stress-induced intrinsic apoptotic signaling pathway response to stimulus negative regulation of neuron apoptotic process signaling negative regulation of signaling negative regulation of intracellular signal transduction negative regulation of biological process regulation of signal transduction regulation of programmed cell death regulation of intrinsic apoptotic signaling pathway intracellular signal transduction negative regulation of cell communication cell communication regulation of intracellular signal transduction negative regulation of apoptotic signaling pathway negative regulation of cellular process signal transduction intrinsic apoptotic signaling pathway regulation of oxidative stress-induced neuron intrinsic apoptotic signaling pathway regulation of biological process regulation of signaling negative regulation of response to stimulus negative regulation of programmed cell death regulation of apoptotic process negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway cell death negative regulation of signal transduction neuron intrinsic apoptotic signaling pathway in response to oxidative stress apoptotic signaling pathway negative regulation of intrinsic apoptotic signaling pathway negative regulation of apoptotic process regulation of response to stimulus negative regulation of oxidative stress-induced neuron intrinsic apoptotic signaling pathway regulation of cell communication apoptotic process programmed cell death regulation of neuron apoptotic process regulation of apoptotic signaling pathway response to oxidative stress cellular response to chemical stimulus cellular response to stress response to stress response to chemical cellular response to oxidative stress cellular response to chemical stress	membrane-bounded organelle intracellular organelle intracellular anatomical structure mitochondrion organelle cytoplasm cellular anatomical entity intracellular membrane-bounded organelle membrane-enclosed lumen mitochondrial matrix intracellular organelle lumen organelle lumen

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D, E	IPR000304	Pyrroline-5-carboxylate reductase	Family
A, B, C, D, E	IPR008927	6-phosphogluconate dehydrogenase-like, C-terminal domain superfamily	Homologous Superfamily
A, B, C, D, E	IPR028939	Pyrroline-5-carboxylate reductase, catalytic, N-terminal	Domain
A, B, C, D, E	IPR036291	NAD(P)-binding domain superfamily	Homologous Superfamily
A, B, C, D, E	IPR029036	Pyrroline-5-carboxylate reductase, dimerisation domain	Domain

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, B, C, D, E	Pharos: P32322	cutis laxa Hutchinson-Gilford progeria syndrome autosomal recessive cutis laxa type 2B PYCR1-related de Barsy syndrome Liver Cirrhosis, Experimental geroderma osteodysplastica ovarian cancer Sjogren syndrome attention deficit hyperactivity disorder, inattentive type breast carcinoma ductal breast carcinoma in situ large cell medulloblastoma lung cancer osteogenesis imperfecta psoriasis cutis laxa Hutchinson-Gilford progeria syndrome autosomal recessive cutis laxa type 2B PYCR1-related de Barsy syndrome Liver Cirrhosis, Experimental geroderma osteodysplastica ovarian cancer Sjogren syndrome attention deficit hyperactivity disorder, inattentive type breast carcinoma ductal breast carcinoma in situ large cell medulloblastoma lung cancer osteogenesis imperfecta psoriasis breast fibroadenoma Ehlers-Danlos syndrome intellectual disability osteosarcoma breast cancer invasive ductal breast carcinoma lung adenocarcinoma non-small cell lung carcinoma

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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 R01GM133198.