1ZY0

X-ray structure of peptide deformylase from Arabidopsis thaliana (AtPDF1A); crystals grown in PEG-6000

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation
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	d1zy0a1	Alpha and beta proteins (a+b)	Peptide deformylase	Peptide deformylase	automated matches	automated matches	thale cress (Arabidopsis thaliana ) [TaxId: 3702 ],	SCOPe (2.08)
A	d1zy0a2	Artifacts	Tags	Tags	Tags	C-terminal Tags	thale cress (Arabidopsis thaliana ) [TaxId: 3702 ],	SCOPe (2.08)
B	d1zy0b1	Alpha and beta proteins (a+b)	Peptide deformylase	Peptide deformylase	automated matches	automated matches	thale cress (Arabidopsis thaliana ) [TaxId: 3702 ],	SCOPe (2.08)
B	d1zy0b2	Artifacts	Tags	Tags	Tags	C-terminal Tags	thale cress (Arabidopsis thaliana ) [TaxId: 3702 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	Peptide deformylase	8064310	3001229	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Peptide deformylase	8064310	3001229	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	Pep_deformylase	e1zy0A1	A: a+b complex topology	X: Peptide deformylase (From Topology)	H: Peptide deformylase (From Topology)	T: Peptide deformylase	F: Pep_deformylase	ECOD (1.6)
B	Pep_deformylase	e1zy0B1	A: a+b complex topology	X: Peptide deformylase (From Topology)	H: Peptide deformylase (From Topology)	T: Peptide deformylase	F: Pep_deformylase	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.90.45.10	Alpha Beta	Alpha-Beta Complex	Peptide Deformylase	Peptide deformylase	CATH (4.3.0)
B	3.90.45.10	Alpha Beta	Alpha-Beta Complex	Peptide Deformylase	Peptide deformylase	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B	PF01327	Polypeptide deformylase (Pep_deformylase)	Polypeptide deformylase	-	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B	Peptide deformylase, mitochondrial	peptide deformylase activity hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amides hydrolase activity catalytic activity hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds cation binding ion binding binding metal ion binding small molecule binding	macromolecule modification metabolic process primary metabolic process protein metabolic process macromolecule metabolic process protein modification process co-translational protein modification cellular biosynthetic process cellular metabolic process translation gene expression macromolecule biosynthetic process biosynthetic process cellular process	membrane-bounded organelle intracellular organelle intracellular anatomical structure mitochondrion organelle cytoplasm cellular anatomical entity intracellular membrane-bounded organelle plastid chloroplast plastid stroma chloroplast stroma cell periphery external encapsulating structure membrane-bounded organelle intracellular organelle intracellular anatomical structure mitochondrion organelle cytoplasm cellular anatomical entity intracellular membrane-bounded organelle plastid chloroplast plastid stroma chloroplast stroma cell periphery external encapsulating structure plant-type cell wall cell wall

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR023635	Peptide deformylase	Family
A, B	IPR036821	Peptide deformylase superfamily	Homologous Superfamily

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.