4DR8

Crystal structure of a peptide deformylase from Synechococcus elongatus

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	d4dr8a_	Alpha and beta proteins (a+b)	Peptide deformylase	Peptide deformylase	automated matches	automated matches	(Synechococcus elongatus PCC 6301 ) [TaxId: 269084 ],	SCOPe (2.08)
B	d4dr8b_	Alpha and beta proteins (a+b)	Peptide deformylase	Peptide deformylase	automated matches	automated matches	(Synechococcus elongatus PCC 6301 ) [TaxId: 269084 ],	SCOPe (2.08)
D	d4dr8d_	Alpha and beta proteins (a+b)	Peptide deformylase	Peptide deformylase	automated matches	automated matches	(Synechococcus elongatus PCC 6301 ) [TaxId: 269084 ],	SCOPe (2.08)
C	d4dr8c_	Alpha and beta proteins (a+b)	Peptide deformylase	Peptide deformylase	automated matches	automated matches	(Synechococcus elongatus PCC 6301 ) [TaxId: 269084 ],	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	8074776	3001229	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Peptide deformylase	8074776	3001229	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Peptide deformylase	8074776	3001229	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Peptide deformylase	8074776	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	e4dr8A1	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	e4dr8B1	A: a+b complex topology	X: Peptide deformylase (From Topology)	H: Peptide deformylase (From Topology)	T: Peptide deformylase	F: Pep_deformylase	ECOD (1.6)
D	Pep_deformylase	e4dr8D1	A: a+b complex topology	X: Peptide deformylase (From Topology)	H: Peptide deformylase (From Topology)	T: Peptide deformylase	F: Pep_deformylase	ECOD (1.6)
C	Pep_deformylase	e4dr8C1	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)
D	3.90.45.10	Alpha Beta	Alpha-Beta Complex	Peptide Deformylase	Peptide deformylase	CATH (4.3.0)
C	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, C, D	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, C, D	Peptide deformylase	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	peptidyl-methionine modification macromolecule modification peptidyl-amino acid modification metabolic process cellular process primary metabolic process protein metabolic process macromolecule metabolic process protein modification process biosynthetic process translation gene expression macromolecule biosynthetic process	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D	IPR023635	Peptide deformylase	Family
A, B, C, D	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.