5KOB | pdb_00005kob

Crystal structure of a peptide deformylase from Burkholderia xenovorans

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)
D	d5kobd_	Alpha and beta proteins (a+b)	Peptide deformylase	Peptide deformylase	automated matches	automated matches	(Paraburkholderia xenovorans LB400 ) [TaxId: 266265 ],	SCOPe (2.08)
C	d5kobc_	Alpha and beta proteins (a+b)	Peptide deformylase	Peptide deformylase	automated matches	automated matches	(Paraburkholderia xenovorans LB400 ) [TaxId: 266265 ],	SCOPe (2.08)
B	d5kobb_	Alpha and beta proteins (a+b)	Peptide deformylase	Peptide deformylase	automated matches	automated matches	(Paraburkholderia xenovorans LB400 ) [TaxId: 266265 ],	SCOPe (2.08)
A	d5koba1	Alpha and beta proteins (a+b)	Peptide deformylase	Peptide deformylase	automated matches	automated matches	(Paraburkholderia xenovorans LB400 ) [TaxId: 266265 ],	SCOPe (2.08)
A	d5koba2	Artifacts	Tags	Tags	Tags	N-terminal Tags	(Paraburkholderia xenovorans LB400 ) [TaxId: 266265 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
D	SCOP2 Family	Peptide deformylase	8064323	4002432	SCOP2 (2022-06-29)
D	SCOP2 Superfamily	Peptide deformylase	8064324	3001229	SCOP2 (2022-06-29)
C	SCOP2B Superfamily	Peptide deformylase	8064324	3001229	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Peptide deformylase	8064324	3001229	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Peptide deformylase	8064324	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)
D	Gag_p24_C	e5kobD1	A: a/b three-layered sandwiches	X: MocoBD/DmpA-related	H: MocoBD/DmpA-related	T: Retrovirus capsid protein-C	F: Gag_p24_C	ECOD (v294.1)
C	Gag_p24_C	e5kobC1	A: a/b three-layered sandwiches	X: MocoBD/DmpA-related	H: MocoBD/DmpA-related	T: Retrovirus capsid protein-C	F: Gag_p24_C	ECOD (v294.1)
B	Gag_p24_C	e5kobB1	A: a/b three-layered sandwiches	X: MocoBD/DmpA-related	H: MocoBD/DmpA-related	T: Retrovirus capsid protein-C	F: Gag_p24_C	ECOD (v294.1)
A	Gag_p24_C	e5kobA1	A: a/b three-layered sandwiches	X: MocoBD/DmpA-related	H: MocoBD/DmpA-related	T: Retrovirus capsid protein-C	F: Gag_p24_C	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
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)
B	3.90.45.10	Alpha Beta	Alpha-Beta Complex	Peptide Deformylase	Peptide deformylase	CATH (4.3.0)
A	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	biosynthetic process metabolic process cellular process primary metabolic process protein metabolic process macromolecule metabolic process translation gene expression protein biosynthetic process 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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.