5BWA | pdb_00005bwa

Crystal structure of ODC-PLP-AZ1 ternary complex

External Resource: Annotation

Domain Annotation: SCOP2 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: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	PLP-binding barrel	8043281	3000273	SCOP2B (2022-06-29)
B	SCOP2 Family	Ornithine decarboxylase antizyme-like	8082004	4003929	SCOP2 (2022-06-29)
B	SCOP2 Superfamily	AZ1 domain-like	8082005	3002482	SCOP2 (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		e5bwaA1	A: Membrane attack complex/perforin (MACPF) and cholesterol-dependent cytolysin (CDC) domains	X: Snake toxin-like	H: Snake toxin-like	T:	F:	ECOD (20:10:01)
B		e5bwaB1	A: Membrane attack complex/perforin (MACPF) and cholesterol-dependent cytolysin (CDC) domains	X: Snake toxin-like	H: Snake toxin-like	T:	F:	ECOD (20:10:01)

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	3.40.630.60	Alpha Beta	3-Layer(aba) Sandwich	Aminopeptidase		CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	PF02784	Pyridoxal-dependent decarboxylase, pyridoxal binding domain (Orn_Arg_deC_N)	Pyridoxal-dependent decarboxylase, pyridoxal binding domain	These pyridoxal-dependent decarboxylases acting on ornithine, lysine, arginine and related substrates This domain has a TIM barrel fold.	Domain
A	PF00278	Pyridoxal-dependent decarboxylase, C-terminal sheet domain (Orn_DAP_Arg_deC)	Pyridoxal-dependent decarboxylase, C-terminal sheet domain	These pyridoxal-dependent decarboxylases act on ornithine, lysine, arginine and related substrates.	Domain
B	PF02100	Ornithine decarboxylase antizyme (ODC_AZ)	Ornithine decarboxylase antizyme	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	Ornithine decarboxylase	identical protein binding protein binding binding protein homodimerization activity protein dimerization activity ornithine decarboxylase activity carboxy-lyase activity lyase activity catalytic activity carbon-carbon lyase activity	regulation of biological process cell population proliferation regulation of cellular process positive regulation of cell population proliferation regulation of cell population proliferation biological regulation positive regulation of biological process cellular process positive regulation of cellular process amine metabolic process metabolic process polyamine metabolic process biogenic amine metabolic process oxoacid metabolic process regulation of biological process cell population proliferation regulation of cellular process positive regulation of cell population proliferation regulation of cell population proliferation biological regulation positive regulation of biological process cellular process positive regulation of cellular process amine metabolic process metabolic 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 biogenic amine biosynthetic 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 biosynthetic process amine biosynthetic process polyamine biosynthetic process putrescine biosynthetic process from arginine catabolic process regulation of protein metabolic process regulation of macromolecule metabolic process protein catabolic process regulation of catabolic process macromolecule catabolic process regulation of primary metabolic process protein metabolic process macromolecule metabolic process regulation of metabolic process regulation of protein catabolic process biological process involved in interspecies interaction between organisms response to stimulus response to other organism response to external stimulus response to external biotic stimulus response to virus response to biotic stimulus developmental process multicellular organism development multicellular organismal process anatomical structure development animal organ development kidney development renal system development system development	cellular anatomical structure intracellular anatomical structure cytoplasm cytosol
B	Ornithine decarboxylase antizyme 1	enzyme regulator activity molecular function inhibitor activity ornithine decarboxylase regulator activity molecular function regulator activity enzyme inhibitor activity ornithine decarboxylase inhibitor 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 viral gene expression viral process viral translational frameshifting viral translation regulation of localization 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 viral gene expression viral process viral translational frameshifting viral translation regulation of localization regulation of polyamine transmembrane transport regulation of biological process nitrogen compound transport regulation of cellular process negative regulation of polyamine transmembrane transport transport regulation of transport biological regulation negative regulation of biological process negative regulation of transport establishment of localization negative regulation of transmembrane transport transmembrane transport polyamine transmembrane transport localization regulation of transmembrane transport negative regulation of cellular process polyamine transport catabolic process positive regulation of protein metabolic process positive regulation of biological process macromolecule catabolic process regulation of primary metabolic process positive regulation of metabolic process positive regulation of macromolecule metabolic process protein metabolic process positive regulation of cellular process regulation of protein metabolic process primary metabolic process regulation of macromolecule metabolic process protein catabolic process regulation of catabolic process positive regulation of protein catabolic process positive regulation of catabolic process macromolecule metabolic process regulation of metabolic process regulation of protein catabolic process establishment of protein localization cellular localization regulation of protein localization positive regulation of establishment of protein localization positive regulation of protein transport establishment of localization in cell positive regulation of intracellular transport intracellular protein localization regulation of intracellular transport regulation of establishment of protein localization intracellular transport regulation of protein transport positive regulation of transport protein transport regulation of cellular localization macromolecule localization positive regulation of protein localization regulation of intracellular protein transport positive regulation of intracellular protein transport intracellular protein transport	cellular anatomical structure intracellular anatomical structure cytoplasm cytosol membrane-bounded organelle intracellular organelle organelle nucleus intracellular membrane-bounded organelle

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR002433	Ornithine decarboxylase	Family
A	IPR029066	PLP-binding barrel	Homologous Superfamily
A	IPR022644	Orn/DAP/Arg decarboxylase 2, N-terminal	Domain
A	IPR022653	Orn/DAP/Arg decarboxylase 2, pyridoxal-phosphate binding site	Binding Site
A	IPR022643	Orn/DAP/Arg decarboxylase 2, C-terminal	Domain
A	IPR009006	Alanine racemase/group IV decarboxylase, C-terminal	Homologous Superfamily
A	IPR000183	Ornithine/DAP/Arg decarboxylase	Family
A	IPR022657	Orn/DAP/Arg decarboxylase 2, conserved site	Conserved Site
B	IPR038581	Ornithine decarboxylase antizyme superfamily	Homologous Superfamily
B	IPR002993	Ornithine decarboxylase antizyme	Family
B	IPR016181	Acyl-CoA N-acyltransferase	Homologous Superfamily

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A	Pharos: P11926	papilloma malignant colon neoplasm colorectal cancer HIV infectious disease skin cancer squamous papilloma skin neoplasm lung cancer malignant glioma oligodendroglioma astrocytic tumor plasma cell myeloma benign colon neoplasm sinusitis colorectal carcinoma papilloma malignant colon neoplasm colorectal cancer HIV infectious disease skin cancer squamous papilloma skin neoplasm lung cancer malignant glioma oligodendroglioma astrocytic tumor plasma cell myeloma benign colon neoplasm sinusitis colorectal carcinoma spina bifida dermatomyositis Female Facial Hirsutism invasive ductal breast carcinoma medulloblastoma ovarian cancer papillomatosis atypical teratoid rhabdoid tumor primitive neuroectodermal tumor colonic neoplasm diabetes mellitus glioblastoma human African trypanosomiasis large cell medulloblastoma malignant ependymoma myopathy pancreatic ductal adenocarcinoma pituitary cancer Barrett esophagus psoriasis cutaneous lupus erythematosus ulcerative colitis esophageal adenocarcinoma hypotrichosis
B	Pharos: P54368	atypical teratoid rhabdoid tumor lymphoplasmacytic lymphoma plasma cell myeloma diabetes mellitus ovarian cancer lung cancer pancreatic intraductal papillary-mucinous neoplasm

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.