4PXH | pdb_00004pxh

Structure of P450sky (CYP163B3), a cytochrome P450 from skyllamycin biosynthesis in complex with a peptidyl carrier protein domain

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
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)
F	d4pxhf1	All alpha proteins	Acyl carrier protein-like	ACP-like	automated matches	automated matches	(Streptomyces sp. Acta 2897 ) [TaxId: 1001349 ],	SCOPe (2.08)
F	d4pxhf2	Artifacts	Tags	Tags	Tags	C-terminal Tags	(Streptomyces sp. Acta 2897 ) [TaxId: 1001349 ],	SCOPe (2.08)
D	d4pxhd1	All alpha proteins	Acyl carrier protein-like	ACP-like	automated matches	automated matches	(Streptomyces sp. Acta 2897 ) [TaxId: 1001349 ],	SCOPe (2.08)
D	d4pxhd2	Artifacts	Tags	Tags	Tags	C-terminal Tags	(Streptomyces sp. Acta 2897 ) [TaxId: 1001349 ],	SCOPe (2.08)
B	d4pxhb1	All alpha proteins	Acyl carrier protein-like	ACP-like	automated matches	automated matches	(Streptomyces sp. Acta 2897 ) [TaxId: 1001349 ],	SCOPe (2.08)
B	d4pxhb2	Artifacts	Tags	Tags	Tags	C-terminal Tags	(Streptomyces sp. Acta 2897 ) [TaxId: 1001349 ],	SCOPe (2.08)
E	d4pxhe_	All alpha proteins	Cytochrome P450	Cytochrome P450	automated matches	automated matches	(Streptomyces sp. Acta 2897 ) [TaxId: 1001349 ],	SCOPe (2.08)
C	d4pxhc_	All alpha proteins	Cytochrome P450	Cytochrome P450	automated matches	automated matches	(Streptomyces sp. Acta 2897 ) [TaxId: 1001349 ],	SCOPe (2.08)
A	d4pxha_	All alpha proteins	Cytochrome P450	Cytochrome P450	automated matches	automated matches	(Streptomyces sp. Acta 2897 ) [TaxId: 1001349 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
F	SCOP2B Superfamily	ACP-like	8064130	3001805	SCOP2B (2022-06-29)
D	SCOP2 Family	Peptidyl carrier domain	8064129	4000860	SCOP2 (2022-06-29)
D	SCOP2 Superfamily	ACP-like	8064130	3001805	SCOP2 (2022-06-29)
B	SCOP2B Superfamily	ACP-like	8064130	3001805	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	Cytochrome P450	8080145	3001061	SCOP2B (2022-06-29)
C	SCOP2 Family	Cytochrome P450	8080144	4001206	SCOP2 (2022-06-29)
C	SCOP2 Superfamily	Cytochrome P450	8080145	3001061	SCOP2 (2022-06-29)
A	SCOP2B Superfamily	Cytochrome P450	8080145	3001061	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)
F	RNase_T	e4pxhF1	A: alpha bundles	X: alpha/beta-Hydrolases	H: alpha/beta-Hydrolases	T: alpha/beta-Hydrolases	F: RNase_T	ECOD (develop294)
D	RNase_T	e4pxhD1	A: alpha bundles	X: alpha/beta-Hydrolases	H: alpha/beta-Hydrolases	T: alpha/beta-Hydrolases	F: RNase_T	ECOD (develop294)
B	RNase_T	e4pxhB1	A: alpha bundles	X: alpha/beta-Hydrolases	H: alpha/beta-Hydrolases	T: alpha/beta-Hydrolases	F: RNase_T	ECOD (develop294)
E	RNase_T	e4pxhE1	A: alpha bundles	X: alpha/beta-Hydrolases	H: alpha/beta-Hydrolases	T: alpha/beta-Hydrolases	F: RNase_T	ECOD (develop294)
C	RNase_T	e4pxhC1	A: alpha bundles	X: alpha/beta-Hydrolases	H: alpha/beta-Hydrolases	T: alpha/beta-Hydrolases	F: RNase_T	ECOD (develop294)
A	Ribosomal_S8e	e4pxhA1	A: alpha bundles	X: Immunoglobulin-like beta-sandwich	H: Ribosomal protein L14-related	T: Ribosomal protein L14-related	F: Ribosomal_S8e	ECOD (develop294)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
F	1.10.1200.10	Mainly Alpha	Orthogonal Bundle	Non-ribosomal Peptide Synthetase Peptidyl Carrier Protein	Chain A	CATH (4.3.0)
D	1.10.1200.10	Mainly Alpha	Orthogonal Bundle	Non-ribosomal Peptide Synthetase Peptidyl Carrier Protein	Chain A	CATH (4.3.0)
B	1.10.1200.10	Mainly Alpha	Orthogonal Bundle	Non-ribosomal Peptide Synthetase Peptidyl Carrier Protein	Chain A	CATH (4.3.0)
E	1.10.630.10	Mainly Alpha	Orthogonal Bundle	Cytochrome p450	Cytochrome P450	CATH (4.3.0)
C	1.10.630.10	Mainly Alpha	Orthogonal Bundle	Cytochrome p450	Cytochrome P450	CATH (4.3.0)
A	1.10.630.10	Mainly Alpha	Orthogonal Bundle	Cytochrome p450	Cytochrome P450	CATH (4.3.0)

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
B, D, F	Peptide synthetase	vitamin binding modified amino acid binding binding ion binding anion binding phosphopantetheine binding sulfur compound binding small molecule binding catalytic activity	secondary metabolite biosynthetic process biosynthetic process metabolic process cellular process secondary metabolic process monocarboxylic acid biosynthetic process small molecule biosynthetic process oxoacid metabolic process carboxylic acid metabolic process organic acid biosynthetic process organic acid metabolic process carboxylic acid biosynthetic process small molecule metabolic process monocarboxylic acid metabolic process secondary metabolite biosynthetic process biosynthetic process metabolic process cellular process secondary metabolic process monocarboxylic acid biosynthetic process small molecule biosynthetic process oxoacid metabolic process carboxylic acid metabolic process organic acid biosynthetic process organic acid metabolic process carboxylic acid biosynthetic process small molecule metabolic process monocarboxylic acid metabolic process lipid biosynthetic process primary metabolic process lipid metabolic process antibiotic metabolic process antibiotic biosynthetic process amino acid activation peptide biosynthetic process amino acid activation for nonribosomal peptide biosynthetic process amino acid metabolic process nonribosomal peptide biosynthetic process peptide metabolic process	cellular anatomical structure intracellular anatomical structure cytoplasm
A, C, E	P450 monooxygenase	oxidoreductase activity monooxygenase activity oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, NAD(P)H as one donor, and incorporation of one atom of oxygen catalytic activity cholest-4-en-3-one 26-monooxygenase activity binding tetrapyrrole binding heme binding steroid hydroxylase activity cation binding transition metal ion binding iron ion binding ion binding oxidoreductase activity monooxygenase activity oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, NAD(P)H as one donor, and incorporation of one atom of oxygen catalytic activity cholest-4-en-3-one 26-monooxygenase activity binding tetrapyrrole binding heme binding steroid hydroxylase activity cation binding transition metal ion binding iron ion binding ion binding metal ion binding small molecule binding	sterol catabolic process alcohol catabolic process catabolic process lipid catabolic process sterol metabolic process steroid metabolic process cholesterol metabolic process alcohol metabolic process primary metabolic process cholesterol catabolic process secondary alcohol metabolic process steroid catabolic process small molecule metabolic process metabolic process sterol catabolic process alcohol catabolic process catabolic process lipid catabolic process sterol metabolic process steroid metabolic process cholesterol metabolic process alcohol metabolic process primary metabolic process cholesterol catabolic process secondary alcohol metabolic process steroid catabolic process small molecule metabolic process metabolic process cellular process small molecule catabolic process lipid metabolic process	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
B, D, F	IPR006162	Phosphopantetheine attachment site	PTM
B, D, F	IPR009081	Phosphopantetheine binding ACP domain	Domain
B, D, F	IPR020806	Polyketide synthase-like, phosphopantetheine-binding domain	Domain
B, D, F	IPR045851	AMP-binding enzyme domain superfamily	Homologous Superfamily
B, D, F	IPR010071	Amino acid adenylation domain	Domain
B, D, F	IPR020845	AMP-binding, conserved site	Conserved Site
B, D, F	IPR023213	Chloramphenicol acetyltransferase-like domain superfamily	Homologous Superfamily
B, D, F	IPR010060	Non-ribosomal peptide synthase	Domain
B, D, F	IPR042099	ANL, N-terminal domain	Homologous Superfamily
B, D, F	IPR001242	Condensation domain	Domain
B, D, F	IPR036736	ACP-like superfamily	Homologous Superfamily
B, D, F	IPR025110	AMP-binding enzyme, C-terminal domain	Domain
B, D, F	IPR000873	AMP-dependent synthetase/ligase domain	Domain
A, C, E	IPR017972	Cytochrome P450, conserved site	Conserved Site
A, C, E	IPR001128	Cytochrome P450	Family
A, C, E	IPR002397	Cytochrome P450, B-class	Family
A, C, E	IPR036396	Cytochrome P450 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.