3EQ1 | pdb_00003eq1

The Crystal Structure of Human Porphobilinogen Deaminase at 2.8A resolution

External Resource: Annotation

Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Pharos: Disease Associations

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
B	Porphobil_deamC	e3eq1B1	A: a+b two layers	X: dsRBD-like	H: Porphobilinogen deaminase (hydroxymethylbilane synthase), C-terminal domain (From Topology)	T: Porphobilinogen deaminase (hydroxymethylbilane synthase), C-terminal domain	F: Porphobil_deamC	ECOD (1.6)
B	Porphobil_deam_N	e3eq1B2	A: a/b three-layered sandwiches	X: Periplasmic binding protein-like II (From Topology)	H: Periplasmic binding protein-like II (From Topology)	T: Periplasmic binding protein-like II	F: Porphobil_deam_N	ECOD (1.6)
B	Porphobil_deam_C	e3eq1B3	A: a/b three-layered sandwiches	X: Periplasmic binding protein-like II (From Topology)	H: Periplasmic binding protein-like II (From Topology)	T: Periplasmic binding protein-like II	F: Porphobil_deam_C	ECOD (1.6)
A	Porphobil_deamC	e3eq1A1	A: a+b two layers	X: dsRBD-like	H: Porphobilinogen deaminase (hydroxymethylbilane synthase), C-terminal domain (From Topology)	T: Porphobilinogen deaminase (hydroxymethylbilane synthase), C-terminal domain	F: Porphobil_deamC	ECOD (1.6)
A	Porphobil_deam_N	e3eq1A2	A: a/b three-layered sandwiches	X: Periplasmic binding protein-like II (From Topology)	H: Periplasmic binding protein-like II (From Topology)	T: Periplasmic binding protein-like II	F: Porphobil_deam_N	ECOD (1.6)
A	Porphobil_deam_C	e3eq1A3	A: a/b three-layered sandwiches	X: Periplasmic binding protein-like II (From Topology)	H: Periplasmic binding protein-like II (From Topology)	T: Periplasmic binding protein-like II	F: Porphobil_deam_C	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
B	3.40.190.10	Alpha Beta	3-Layer(aba) Sandwich	D-Maltodextrin-Binding Protein	domain 2	CATH (4.3.0)
B	3.30.160.40	Alpha Beta	2-Layer Sandwich	Double Stranded RNA Binding Domain	Porphobilinogen deaminase, C-terminal domain	CATH (4.3.0)
A	3.40.190.10	Alpha Beta	3-Layer(aba) Sandwich	D-Maltodextrin-Binding Protein	domain 2	CATH (4.3.0)
A	3.30.160.40	Alpha Beta	2-Layer Sandwich	Double Stranded RNA Binding Domain	Porphobilinogen deaminase, C-terminal domain	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B	PF03900	Porphobilinogen deaminase, C-terminal domain (Porphobil_deamC)	Porphobilinogen deaminase, C-terminal domain		Domain
A, B	PF01379	Porphobilinogen deaminase, dipyromethane cofactor binding domain (Porphobil_deam)	Porphobilinogen deaminase, dipyromethane cofactor binding domain		Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B	Porphobilinogen deaminase	hydroxymethylbilane synthase activity transferase activity transferase activity, transferring alkyl or aryl (other than methyl) groups catalytic activity	heme A biosynthetic process heme metabolic process pigment metabolic process porphyrin-containing compound biosynthetic process tetrapyrrole metabolic process heme biosynthetic process pigment biosynthetic process tetrapyrrole biosynthetic process biosynthetic process metabolic process cellular process porphyrin-containing compound metabolic process heme O biosynthetic process protoporphyrinogen IX metabolic process heme A biosynthetic process heme metabolic process pigment metabolic process porphyrin-containing compound biosynthetic process tetrapyrrole metabolic process heme biosynthetic process pigment biosynthetic process tetrapyrrole biosynthetic process biosynthetic process metabolic process cellular process porphyrin-containing compound metabolic process heme O biosynthetic process protoporphyrinogen IX metabolic process protoporphyrinogen IX biosynthetic process heme B biosynthetic process	cellular anatomical structure intracellular anatomical structure cytoplasm cytosol

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR022418	Porphobilinogen deaminase, C-terminal	Domain
A, B	IPR000860	Porphobilinogen deaminase	Family
A, B	IPR022419	Porphobilinogen deaminase, dipyrromethane cofactor binding site	Binding Site
A, B	IPR036803	Porphobilinogen deaminase, C-terminal domain superfamily	Homologous Superfamily
A, B	IPR022417	Porphobilinogen deaminase, N-terminal	Domain

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, B	Pharos: P08397	acute intermittent porphyria inherited porphyria Porphyria, Acute Intermittent, Nonerythroid Variant atypical teratoid rhabdoid tumor heart disease large cell medulloblastoma lung cancer oligodendroglioma psoriasis acute interstitial pneumonia hepatic porphyria inborn errors of metabolism leukodystrophy malignant ependymoma osteosarcoma acute intermittent porphyria inherited porphyria Porphyria, Acute Intermittent, Nonerythroid Variant atypical teratoid rhabdoid tumor heart disease large cell medulloblastoma lung cancer oligodendroglioma psoriasis acute interstitial pneumonia hepatic porphyria inborn errors of metabolism leukodystrophy malignant ependymoma osteosarcoma variegate porphyria astrocytic tumor glioblastoma hereditary coproporphyria lung adenocarcinoma malignant mesothelioma

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.