6XP1 | pdb_00006xp1

Structure of human PYCR1 complexed with L-thiazolidine-2-carboxylate

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: ECOD Classification
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)
B	d6xp1b2	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	d6xp1b1	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	d6xp1b3	Artifacts	Tags	Tags	Tags	N-terminal Tags	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
C	d6xp1c2	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	d6xp1c1	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	d6xp1d2	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	d6xp1d1	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	d6xp1d3	Artifacts	Tags	Tags	Tags	N-terminal Tags	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
E	d6xp1e2	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	d6xp1e1	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	d6xp1e3	Artifacts	Tags	Tags	Tags	N-terminal Tags	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
A	d6xp1a2	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	d6xp1a1	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)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
B	P5CR_dimer	e6xp1B1	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	e6xp1B2	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	e6xp1C2	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	e6xp1C1	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	e6xp1D2	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	e6xp1D1	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	e6xp1E1	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	e6xp1E2	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)
A	P5CR_dimer	e6xp1A1	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	e6xp1A2	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)

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, mitochondrial	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 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 small molecule metabolic process small molecule biosynthetic process carboxylic acid metabolic process primary metabolic process glutamine family amino acid biosynthetic process oxoacid metabolic 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 small molecule metabolic process small molecule biosynthetic process carboxylic acid metabolic process primary metabolic process L-amino acid biosynthetic process L-amino acid metabolic process proteinogenic amino acid metabolic process amino acid biosynthetic process 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 cellular anatomical structure intracellular anatomical structure mitochondrion organelle cytoplasm 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	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	IPR053790	Pyrroline-5-carboxylate reductase-like conserved site	Conserved Site
A, B, C, D, E	IPR000304	Pyrroline-5-carboxylate reductase-like	Family
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 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.