1JYM | pdb_00001jym

Crystals of Peptide Deformylase from Plasmodium falciparum with Ten Subunits per Asymmetric Unit Reveal Critical Characteristics of the Active Site for Drug Design

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	d1jyma1	Alpha and beta proteins (a+b)	Peptide deformylase	Peptide deformylase	Peptide deformylase	Peptide deformylase	malaria parasite P. falciparum (Plasmodium falciparum ) [TaxId: 5833 ],	SCOPe (2.08)
A	d1jyma2	Artifacts	Tags	Tags	Tags	C-terminal Tags	malaria parasite P. falciparum (Plasmodium falciparum ) [TaxId: 5833 ],	SCOPe (2.08)
B	d1jymb1	Alpha and beta proteins (a+b)	Peptide deformylase	Peptide deformylase	Peptide deformylase	Peptide deformylase	malaria parasite P. falciparum (Plasmodium falciparum ) [TaxId: 5833 ],	SCOPe (2.08)
B	d1jymb2	Artifacts	Tags	Tags	Tags	C-terminal Tags	malaria parasite P. falciparum (Plasmodium falciparum ) [TaxId: 5833 ],	SCOPe (2.08)
C	d1jymc_	Alpha and beta proteins (a+b)	Peptide deformylase	Peptide deformylase	Peptide deformylase	Peptide deformylase	malaria parasite P. falciparum (Plasmodium falciparum ) [TaxId: 5833 ],	SCOPe (2.08)
D	d1jymd_	Alpha and beta proteins (a+b)	Peptide deformylase	Peptide deformylase	Peptide deformylase	Peptide deformylase	malaria parasite P. falciparum (Plasmodium falciparum ) [TaxId: 5833 ],	SCOPe (2.08)
E	d1jyme1	Alpha and beta proteins (a+b)	Peptide deformylase	Peptide deformylase	Peptide deformylase	Peptide deformylase	malaria parasite P. falciparum (Plasmodium falciparum ) [TaxId: 5833 ],	SCOPe (2.08)
E	d1jyme2	Artifacts	Tags	Tags	Tags	C-terminal Tags	malaria parasite P. falciparum (Plasmodium falciparum ) [TaxId: 5833 ],	SCOPe (2.08)
F	d1jymf_	Alpha and beta proteins (a+b)	Peptide deformylase	Peptide deformylase	Peptide deformylase	Peptide deformylase	malaria parasite P. falciparum (Plasmodium falciparum ) [TaxId: 5833 ],	SCOPe (2.08)
G	d1jymg_	Alpha and beta proteins (a+b)	Peptide deformylase	Peptide deformylase	Peptide deformylase	Peptide deformylase	malaria parasite P. falciparum (Plasmodium falciparum ) [TaxId: 5833 ],	SCOPe (2.08)
H	d1jymh_	Alpha and beta proteins (a+b)	Peptide deformylase	Peptide deformylase	Peptide deformylase	Peptide deformylase	malaria parasite P. falciparum (Plasmodium falciparum ) [TaxId: 5833 ],	SCOPe (2.08)
I	d1jymi_	Alpha and beta proteins (a+b)	Peptide deformylase	Peptide deformylase	Peptide deformylase	Peptide deformylase	malaria parasite P. falciparum (Plasmodium falciparum ) [TaxId: 5833 ],	SCOPe (2.08)
J	d1jymj_	Alpha and beta proteins (a+b)	Peptide deformylase	Peptide deformylase	Peptide deformylase	Peptide deformylase	malaria parasite P. falciparum (Plasmodium falciparum ) [TaxId: 5833 ],	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	8040755	3001229	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Peptide deformylase	8040755	3001229	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Peptide deformylase	8040755	3001229	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Peptide deformylase	8040755	3001229	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	Peptide deformylase	8040755	3001229	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	Peptide deformylase	8040755	3001229	SCOP2B (2022-06-29)
G	SCOP2B Superfamily	Peptide deformylase	8040755	3001229	SCOP2B (2022-06-29)
H	SCOP2B Superfamily	Peptide deformylase	8040755	3001229	SCOP2B (2022-06-29)
I	SCOP2B Superfamily	Peptide deformylase	8040755	3001229	SCOP2B (2022-06-29)
J	SCOP2B Superfamily	Peptide deformylase	8040755	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		e1jymA1	A: C-terminal subdomain in Lon-related proteases catalytic domains	X: C-terminal subdomain in Lon-related proteases catalytic domains	H: C-terminal subdomain in Lon-related proteases catalytic domains	T: CBAH	F:	ECOD (20:10:01)
B		e1jymB1	A: C-terminal subdomain in Lon-related proteases catalytic domains	X: C-terminal subdomain in Lon-related proteases catalytic domains	H: C-terminal subdomain in Lon-related proteases catalytic domains	T: CBAH	F:	ECOD (20:10:01)
C		e1jymC1	A: C-terminal subdomain in Lon-related proteases catalytic domains	X: C-terminal subdomain in Lon-related proteases catalytic domains	H: C-terminal subdomain in Lon-related proteases catalytic domains	T: CBAH	F:	ECOD (20:10:01)
D		e1jymD1	A: C-terminal subdomain in Lon-related proteases catalytic domains	X: C-terminal subdomain in Lon-related proteases catalytic domains	H: C-terminal subdomain in Lon-related proteases catalytic domains	T: CBAH	F:	ECOD (20:10:01)
E		e1jymE1	A: C-terminal subdomain in Lon-related proteases catalytic domains	X: C-terminal subdomain in Lon-related proteases catalytic domains	H: C-terminal subdomain in Lon-related proteases catalytic domains	T: CBAH	F:	ECOD (20:10:01)
F		e1jymF1	A: C-terminal subdomain in Lon-related proteases catalytic domains	X: C-terminal subdomain in Lon-related proteases catalytic domains	H: C-terminal subdomain in Lon-related proteases catalytic domains	T: CBAH	F:	ECOD (20:10:01)
G		e1jymG1	A: C-terminal subdomain in Lon-related proteases catalytic domains	X: C-terminal subdomain in Lon-related proteases catalytic domains	H: C-terminal subdomain in Lon-related proteases catalytic domains	T: CBAH	F:	ECOD (20:10:01)
H		e1jymH1	A: C-terminal subdomain in Lon-related proteases catalytic domains	X: C-terminal subdomain in Lon-related proteases catalytic domains	H: C-terminal subdomain in Lon-related proteases catalytic domains	T: CBAH	F:	ECOD (20:10:01)
I		e1jymI1	A: C-terminal subdomain in Lon-related proteases catalytic domains	X: C-terminal subdomain in Lon-related proteases catalytic domains	H: C-terminal subdomain in Lon-related proteases catalytic domains	T: CBAH	F:	ECOD (20:10:01)
J		e1jymJ1	A: C-terminal subdomain in Lon-related proteases catalytic domains	X: C-terminal subdomain in Lon-related proteases catalytic domains	H: C-terminal subdomain in Lon-related proteases catalytic domains	T: CBAH	F:	ECOD (20:10:01)

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)
C	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)
E	3.90.45.10	Alpha Beta	Alpha-Beta Complex	Peptide Deformylase	Peptide deformylase	CATH (4.3.0)
F	3.90.45.10	Alpha Beta	Alpha-Beta Complex	Peptide Deformylase	Peptide deformylase	CATH (4.3.0)
G	3.90.45.10	Alpha Beta	Alpha-Beta Complex	Peptide Deformylase	Peptide deformylase	CATH (4.3.0)
H	3.90.45.10	Alpha Beta	Alpha-Beta Complex	Peptide Deformylase	Peptide deformylase	CATH (4.3.0)
I	3.90.45.10	Alpha Beta	Alpha-Beta Complex	Peptide Deformylase	Peptide deformylase	CATH (4.3.0)
J	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, E A, B, C, D, E, F, G, H, I, J	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, E A, B, C, D, E, F, G, H, I, J	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 transition metal ion binding iron ion binding ion binding binding ferrous iron binding metal ion binding small molecule binding	N-terminal protein amino acid modification macromolecule modification metabolic process cellular process primary metabolic process protein metabolic process macromolecule metabolic process protein modification process biosynthetic process translation gene expression protein biosynthetic process macromolecule biosynthetic process	membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure plastid organelle cytoplasm intracellular membrane-bounded organelle apicoplast

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D, E A, B, C, D, E, F, G, H, I, J	IPR023635	Peptide deformylase	Family
A, B, C, D, E A, B, C, D, E, F, G, H, I, J	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.