3G5K | pdb_00003g5k

Structure and activity of human mitochondrial peptide deformylase, a novel cancer target

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	d3g5kd1	Alpha and beta proteins (a+b)	Peptide deformylase	Peptide deformylase	automated matches	automated matches	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
D	d3g5kd2	Artifacts	Tags	Tags	Tags	N-terminal Tags	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
C	d3g5kc1	Alpha and beta proteins (a+b)	Peptide deformylase	Peptide deformylase	automated matches	automated matches	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
C	d3g5kc2	Artifacts	Tags	Tags	Tags	N-terminal Tags	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
B	d3g5kb1	Alpha and beta proteins (a+b)	Peptide deformylase	Peptide deformylase	automated matches	automated matches	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
B	d3g5kb2	Artifacts	Tags	Tags	Tags	N-terminal Tags	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
A	d3g5ka1	Alpha and beta proteins (a+b)	Peptide deformylase	Peptide deformylase	automated matches	automated matches	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
A	d3g5ka2	Artifacts	Tags	Tags	Tags	N-terminal Tags	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
D	SCOP2B Superfamily	Peptide deformylase	8064322	3001229	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Peptide deformylase	8064322	3001229	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Peptide deformylase	8064322	3001229	SCOP2B (2022-06-29)
A	SCOP2 Family	Peptide deformylase	8064321	4002432	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Peptide deformylase	8064322	3001229	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)
D	RdRP_3	e3g5kD1	A: a/b three-layered sandwiches	X: HTH	H: Nudix	T: Nudix	F: RdRP_3	ECOD (v294.1)
C	RdRP_3	e3g5kC1	A: a/b three-layered sandwiches	X: HTH	H: Nudix	T: Nudix	F: RdRP_3	ECOD (v294.1)
B	RdRP_3	e3g5kB1	A: a/b three-layered sandwiches	X: HTH	H: Nudix	T: Nudix	F: RdRP_3	ECOD (v294.1)
A	DUF1968	e3g5kA1	A: a/b three-layered sandwiches	X: TAZ domain	H: EF-hand-related	T: EF-hand	F: DUF1968	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, 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	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 macromolecule modification metabolic process primary metabolic process protein metabolic process macromolecule 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 macromolecule modification metabolic process primary metabolic process protein metabolic process macromolecule metabolic process post-translational protein modification protein modification process peptidyl-methionine modification peptidyl-amino acid modification biosynthetic process translation gene expression protein biosynthetic process macromolecule biosynthetic process	membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure mitochondrion organelle cytoplasm intracellular membrane-bounded organelle

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.

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