1F3T | pdb_00001f3t

CRYSTAL STRUCTURE OF TRYPANOSOMA BRUCEI ORNITHINE DECARBOXYLASE (ODC) COMPLEXED WITH PUTRESCINE, ODC'S REACTION PRODUCT.

External Resource: Annotation

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

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

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A	d1f3ta1	All beta proteins	Domain of alpha and beta subunits of F1 ATP synthase-like	Alanine racemase C-terminal domain-like	Eukaryotic ODC-like	Eukaryotic ornithine decarboxylase (ODC)	(Trypanosoma brucei ) [TaxId: 5691 ],	SCOPe (2.08)
A	d1f3ta2	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	PLP-binding barrel	Alanine racemase-like, N-terminal domain	Eukaryotic ornithine decarboxylase	(Trypanosoma brucei ) [TaxId: 5691 ],	SCOPe (2.08)
B	d1f3tb1	All beta proteins	Domain of alpha and beta subunits of F1 ATP synthase-like	Alanine racemase C-terminal domain-like	Eukaryotic ODC-like	Eukaryotic ornithine decarboxylase (ODC)	(Trypanosoma brucei ) [TaxId: 5691 ],	SCOPe (2.08)
B	d1f3tb2	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	PLP-binding barrel	Alanine racemase-like, N-terminal domain	Eukaryotic ornithine decarboxylase	(Trypanosoma brucei ) [TaxId: 5691 ],	SCOPe (2.08)
C	d1f3tc1	All beta proteins	Domain of alpha and beta subunits of F1 ATP synthase-like	Alanine racemase C-terminal domain-like	Eukaryotic ODC-like	Eukaryotic ornithine decarboxylase (ODC)	(Trypanosoma brucei ) [TaxId: 5691 ],	SCOPe (2.08)
C	d1f3tc2	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	PLP-binding barrel	Alanine racemase-like, N-terminal domain	Eukaryotic ornithine decarboxylase	(Trypanosoma brucei ) [TaxId: 5691 ],	SCOPe (2.08)
D	d1f3td1	All beta proteins	Domain of alpha and beta subunits of F1 ATP synthase-like	Alanine racemase C-terminal domain-like	Eukaryotic ODC-like	Eukaryotic ornithine decarboxylase (ODC)	(Trypanosoma brucei ) [TaxId: 5691 ],	SCOPe (2.08)
D	d1f3td2	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	PLP-binding barrel	Alanine racemase-like, N-terminal domain	Eukaryotic ornithine decarboxylase	(Trypanosoma brucei ) [TaxId: 5691 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	Alanine racemase C-terminal domain-like	8042331	3001044	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Alanine racemase C-terminal domain-like	8042331	3001044	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	PLP-binding barrel	8043283	3000273	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	PLP-binding barrel	8043283	3000273	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Alanine racemase C-terminal domain-like	8042331	3001044	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Alanine racemase C-terminal domain-like	8042331	3001044	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	PLP-binding barrel	8043283	3000273	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Alanine racemase C-terminal domain-like	8042331	3001044	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Alanine racemase C-terminal domain-like	8042331	3001044	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	PLP-binding barrel	8043283	3000273	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Alanine racemase C-terminal domain-like	8042331	3001044	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Alanine racemase C-terminal domain-like	8042331	3001044	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	tRNA-synt_His	e1f3tA1	A: a/b three-layered sandwiches	X: YrdC/RibB	H: SH3	T: SH3	F: tRNA-synt_His	ECOD (v294.1)
B	Glyoxalase	e1f3tB3	A: a/b three-layered sandwiches	X: Fusion glycoprotein F2	H: MoeA-I/Ornithine decarboxylase-C/Reverse ferredoxin-like domain in RNA-polymerase	T: MoeA-I/Ornithine decarboxylase-C/Reverse ferredoxin-like domain in RNA-polymerase	F: Glyoxalase	ECOD (v294.1)
C	Peptidase_S46, Trypsin_2	e1f3tC1	A: a/b three-layered sandwiches	X: Phage tail fiber protein trimerization domain	H: LigT-related	T: LigT-related	F: Peptidase_S46, Trypsin_2	ECOD (v294.1)
C	DUF711	e1f3tC2	A: a/b three-layered sandwiches	X: HTH	H: HTH	T: winged helix domain	F: DUF711	ECOD (v294.1)
D	Peptidase_S46, Trypsin_2	e1f3tD1	A: a/b three-layered sandwiches	X: Phage tail fiber protein trimerization domain	H: LigT-related	T: LigT-related	F: Peptidase_S46, Trypsin_2	ECOD (v294.1)
D	DUF711	e1f3tD2	A: a/b three-layered sandwiches	X: HTH	H: HTH	T: winged helix domain	F: DUF711	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	2.40.37.10	Mainly Beta	Beta Barrel	Lyase, Ornithine Decarboxylase	Chain A, domain 1	CATH (4.3.0)
A	3.20.20.10	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	Alanine racemase	CATH (4.3.0)
B	2.40.37.10	Mainly Beta	Beta Barrel	Lyase, Ornithine Decarboxylase	Chain A, domain 1	CATH (4.3.0)
B	3.20.20.10	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	Alanine racemase	CATH (4.3.0)
C	2.40.37.10	Mainly Beta	Beta Barrel	Lyase, Ornithine Decarboxylase	Chain A, domain 1	CATH (4.3.0)
C	3.20.20.10	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	Alanine racemase	CATH (4.3.0)
D	2.40.37.10	Mainly Beta	Beta Barrel	Lyase, Ornithine Decarboxylase	Chain A, domain 1	CATH (4.3.0)
D	3.20.20.10	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	Alanine racemase	CATH (4.3.0)

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D	ORNITHINE DECARBOXYLASE	ornithine decarboxylase activity carboxy-lyase activity lyase activity catalytic activity carbon-carbon lyase activity	amine metabolic process biogenic amine biosynthetic process biosynthetic process amine biosynthetic process polyamine biosynthetic process metabolic process cellular process polyamine metabolic process biogenic amine metabolic process oxoacid metabolic process amino acid metabolic process organic acid metabolic process alpha-amino acid metabolic process arginine metabolic process amine metabolic process biogenic amine biosynthetic process biosynthetic process amine biosynthetic process polyamine biosynthetic process metabolic process cellular process polyamine metabolic process biogenic amine metabolic process oxoacid metabolic process amino acid metabolic process organic acid metabolic process alpha-amino acid metabolic process arginine metabolic process putrescine metabolic process small molecule metabolic process putrescine biosynthetic process from arginine, via ornithine carboxylic acid metabolic process primary metabolic process L-amino acid metabolic process putrescine biosynthetic process proteinogenic amino acid metabolic process putrescine biosynthetic process from arginine	cellular anatomical structure intracellular anatomical structure cytoplasm

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D	IPR002433	Ornithine decarboxylase	Family
A, B, C, D	IPR029066	PLP-binding barrel	Homologous Superfamily
A, B, C, D	IPR009006	Alanine racemase/group IV decarboxylase, C-terminal	Homologous Superfamily
A, B, C, D	IPR000183	Ornithine/DAP/Arg decarboxylase	Family
A, B, C, D	IPR022644	Orn/DAP/Arg decarboxylase 2, N-terminal	Domain
A, B, C, D	IPR022653	Orn/DAP/Arg decarboxylase 2, pyridoxal-phosphate binding site	Binding Site

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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.