3EJD | pdb_00003ejd

Crystal Structure of P450BioI in complex with hexadec-9Z-enoic acid ligated Acyl Carrier Protein

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)
H	d3ejdh_	All alpha proteins	Cytochrome P450	Cytochrome P450	automated matches	automated matches	(Bacillus subtilis ) [TaxId: 1423 ],	SCOPe (2.08)
F	d3ejdf_	All alpha proteins	Cytochrome P450	Cytochrome P450	automated matches	automated matches	(Bacillus subtilis ) [TaxId: 1423 ],	SCOPe (2.08)
D	d3ejdd_	All alpha proteins	Cytochrome P450	Cytochrome P450	automated matches	automated matches	(Bacillus subtilis ) [TaxId: 1423 ],	SCOPe (2.08)
B	d3ejdb_	All alpha proteins	Cytochrome P450	Cytochrome P450	automated matches	automated matches	(Bacillus subtilis ) [TaxId: 1423 ],	SCOPe (2.08)
G	d3ejdg2	All alpha proteins	Acyl carrier protein-like	ACP-like	Acyl-carrier protein (ACP)	Acyl carrier protein	(Escherichia coli K-12 ) [TaxId: 83333 ],	SCOPe (2.08)
G	d3ejdg3	Artifacts	Tags	Tags	Tags	N-terminal Tags	(Escherichia coli K-12 ) [TaxId: 83333 ],	SCOPe (2.08)
E	d3ejde2	All alpha proteins	Acyl carrier protein-like	ACP-like	Acyl-carrier protein (ACP)	Acyl carrier protein	(Escherichia coli K-12 ) [TaxId: 83333 ],	SCOPe (2.08)
E	d3ejde3	Artifacts	Tags	Tags	Tags	N-terminal Tags	(Escherichia coli K-12 ) [TaxId: 83333 ],	SCOPe (2.08)
C	d3ejdc2	All alpha proteins	Acyl carrier protein-like	ACP-like	Acyl-carrier protein (ACP)	Acyl carrier protein	(Escherichia coli K-12 ) [TaxId: 83333 ],	SCOPe (2.08)
C	d3ejdc3	Artifacts	Tags	Tags	Tags	N-terminal Tags	(Escherichia coli K-12 ) [TaxId: 83333 ],	SCOPe (2.08)
A	d3ejda2	All alpha proteins	Acyl carrier protein-like	ACP-like	Acyl-carrier protein (ACP)	Acyl carrier protein	(Escherichia coli K-12 ) [TaxId: 83333 ],	SCOPe (2.08)
A	d3ejda3	Artifacts	Tags	Tags	Tags	N-terminal Tags	(Escherichia coli K-12 ) [TaxId: 83333 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
H	SCOP2B Superfamily	Cytochrome P450	8078727	3001061	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	Cytochrome P450	8078727	3001061	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Cytochrome P450	8078727	3001061	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Cytochrome P450	8078727	3001061	SCOP2B (2022-06-29)
G	SCOP2B Superfamily	ACP-like	8040084	3001805	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	ACP-like	8040084	3001805	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	ACP-like	8040084	3001805	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	ACP-like	8040084	3001805	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)
H		e3ejdH1	A: HTH	X: HTH	H: tetra-helical, lambda repressor-like	T: FXa_inhibition	F:	ECOD (20:10:01)
F		e3ejdF1	A: HTH	X: HTH	H: tetra-helical, lambda repressor-like	T: FXa_inhibition	F:	ECOD (20:10:01)
D		e3ejdD1	A: HTH	X: HTH	H: tetra-helical, lambda repressor-like	T: FXa_inhibition	F:	ECOD (20:10:01)
B		e3ejdB1	A: HTH	X: HTH	H: tetra-helical, lambda repressor-like	T: FXa_inhibition	F:	ECOD (20:10:01)
G		e3ejdG1	A: C-terminal subdomain in Lon-related proteases catalytic domains	X: p53 tetramerization domain	H: p53 tetramerization domain	T: Cation_efflux	F:	ECOD (20:10:01)
E		e3ejdE1	A: C-terminal subdomain in Lon-related proteases catalytic domains	X: p53 tetramerization domain	H: p53 tetramerization domain	T: Cation_efflux	F:	ECOD (20:10:01)
C		e3ejdC1	A: C-terminal subdomain in Lon-related proteases catalytic domains	X: p53 tetramerization domain	H: p53 tetramerization domain	T: Cation_efflux	F:	ECOD (20:10:01)
A		e3ejdA1	A: C-terminal subdomain in Lon-related proteases catalytic domains	X: p53 tetramerization domain	H: p53 tetramerization domain	T: Cation_efflux	F:	ECOD (20:10:01)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
H	3.30.43.20	Alpha Beta	2-Layer Sandwich	Uridine Diphospho-n-acetylenolpyruvylglucosamine Reductase	domain 2	CATH (4.3.0)
H	1.10.630.10	Mainly Alpha	Orthogonal Bundle	Cytochrome p450	Cytochrome P450	CATH (4.3.0)
F	3.30.43.20	Alpha Beta	2-Layer Sandwich	Uridine Diphospho-n-acetylenolpyruvylglucosamine Reductase	domain 2	CATH (4.3.0)
F	1.10.630.10	Mainly Alpha	Orthogonal Bundle	Cytochrome p450	Cytochrome P450	CATH (4.3.0)
D	3.30.43.20	Alpha Beta	2-Layer Sandwich	Uridine Diphospho-n-acetylenolpyruvylglucosamine Reductase	domain 2	CATH (4.3.0)
D	1.10.630.10	Mainly Alpha	Orthogonal Bundle	Cytochrome p450	Cytochrome P450	CATH (4.3.0)
B	3.30.43.20	Alpha Beta	2-Layer Sandwich	Uridine Diphospho-n-acetylenolpyruvylglucosamine Reductase	domain 2	CATH (4.3.0)
B	1.10.630.10	Mainly Alpha	Orthogonal Bundle	Cytochrome p450	Cytochrome P450	CATH (4.3.0)
G	1.10.1200.10	Mainly Alpha	Orthogonal Bundle	Non-ribosomal Peptide Synthetase Peptidyl Carrier Protein	Chain A	CATH (4.3.0)
E	1.10.1200.10	Mainly Alpha	Orthogonal Bundle	Non-ribosomal Peptide Synthetase Peptidyl Carrier Protein	Chain A	CATH (4.3.0)
C	1.10.1200.10	Mainly Alpha	Orthogonal Bundle	Non-ribosomal Peptide Synthetase Peptidyl Carrier Protein	Chain A	CATH (4.3.0)
A	1.10.1200.10	Mainly Alpha	Orthogonal Bundle	Non-ribosomal Peptide Synthetase Peptidyl Carrier Protein	Chain A	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
B, D, F, H	PF00067	Cytochrome P450 (p450)	Cytochrome P450	Cytochrome P450s are haem-thiolate proteins [6] involved in the oxidative degradation of various compounds. They are particularly well known for their role in the degradation of environmental toxins and mutagens. They can be divided into 4 classes, a ...	Cytochrome P450s are haem-thiolate proteins [6] involved in the oxidative degradation of various compounds. They are particularly well known for their role in the degradation of environmental toxins and mutagens. They can be divided into 4 classes, according to the method by which electrons from NAD(P)H are delivered to the catalytic site. Sequence conservation is relatively low within the family - there are only 3 absolutely conserved residues - but their general topography and structural fold are highly conserved. The conserved core is composed of a coil termed the 'meander', a four-helix bundle, helices J and K, and two sets of beta-sheets. These constitute the haem-binding loop (with an absolutely conserved cysteine that serves as the 5th ligand for the haem iron), the proton-transfer groove and the absolutely conserved EXXR motif in helix K. While prokaryotic P450s are soluble proteins, most eukaryotic P450s are associated with microsomal membranes. their general enzymatic function is to catalyse regiospecific and stereospecific oxidation of non-activated hydrocarbons at physiological temperatures [6].	Domain
A, C, E, G	PF00550	Phosphopantetheine attachment site (PP-binding)	Phosphopantetheine attachment site	A 4'-phosphopantetheine prosthetic group is attached through a serine. This prosthetic group acts as a a 'swinging arm' for the attachment of activated fatty acid and amino-acid groups. This domain forms a four helix bundle. This family includes memb ...	A 4'-phosphopantetheine prosthetic group is attached through a serine. This prosthetic group acts as a a 'swinging arm' for the attachment of activated fatty acid and amino-acid groups. This domain forms a four helix bundle. This family includes members not included in Prosite. The inclusion of these members is supported by sequence analysis and functional evidence. The related domain of Swiss:P19828 has the attachment serine replaced by an alanine.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
B, D, F, H	Biotin biosynthesis cytochrome P450-like enzyme	monooxygenase activity oxidoreductase activity catalytic activity oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen binding tetrapyrrole binding heme binding cation binding transition metal ion binding iron ion binding ion binding metal ion binding small molecule binding	water-soluble vitamin biosynthetic process monocarboxylic acid biosynthetic process biotin metabolic process small molecule biosynthetic process oxoacid metabolic process carboxylic acid metabolic process vitamin biosynthetic process organic acid biosynthetic process organic acid metabolic process biotin biosynthetic process carboxylic acid biosynthetic process vitamin metabolic process sulfur compound biosynthetic process biosynthetic process water-soluble vitamin biosynthetic process monocarboxylic acid biosynthetic process biotin metabolic process small molecule biosynthetic process oxoacid metabolic process carboxylic acid metabolic process vitamin biosynthetic process organic acid biosynthetic process organic acid metabolic process biotin biosynthetic process carboxylic acid biosynthetic process vitamin metabolic process sulfur compound biosynthetic process biosynthetic process small molecule metabolic process metabolic process cellular process sulfur compound metabolic process monocarboxylic acid metabolic process	-
A, C, E, G	Acyl carrier protein	phosphopantetheine-dependent carrier activity prosthetic group binding binding acyl carrier activity molecular carrier activity ACP phosphopantetheine attachment site binding lipid binding vitamin binding modified amino acid binding ion binding anion binding phosphopantetheine binding sulfur compound binding small molecule binding phosphopantetheine-dependent carrier activity prosthetic group binding binding acyl carrier activity molecular carrier activity ACP phosphopantetheine attachment site binding lipid binding vitamin binding modified amino acid binding ion binding anion binding phosphopantetheine binding sulfur compound binding small molecule binding acyl binding	response to stimulus response to chemical response to xenobiotic stimulus fatty acid metabolic process monocarboxylic acid biosynthetic process small molecule biosynthetic process oxoacid metabolic process carboxylic acid metabolic process lipid biosynthetic process primary metabolic process organic acid biosynthetic process organic acid metabolic process fatty acid biosynthetic process carboxylic acid biosynthetic process response to stimulus response to chemical response to xenobiotic stimulus fatty acid metabolic process monocarboxylic acid biosynthetic process small molecule biosynthetic process oxoacid metabolic process carboxylic acid metabolic process lipid biosynthetic process primary metabolic process organic acid biosynthetic process organic acid metabolic process fatty acid biosynthetic process carboxylic acid biosynthetic process biosynthetic process small molecule metabolic process metabolic process cellular process monocarboxylic acid metabolic process lipid metabolic process carbohydrate derivative biosynthetic process lipooligosaccharide metabolic process glycolipid metabolic process lipid A biosynthetic process liposaccharide metabolic process carbohydrate derivative metabolic process glycolipid biosynthetic process phospholipid biosynthetic process phospholipid metabolic process lipid A metabolic process organophosphate metabolic process organophosphate biosynthetic process phosphate-containing compound metabolic process lipooligosaccharide biosynthetic process phosphorus metabolic process	cellular anatomical structure membrane intracellular anatomical structure cytoplasm cytosol

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
B, D, F, H	IPR017972	Cytochrome P450, conserved site	Conserved Site
B, D, F, H	IPR001128	Cytochrome P450	Family
B, D, F, H	IPR002397	Cytochrome P450, B-class	Family
B, D, F, H	IPR036396	Cytochrome P450 superfamily	Homologous Superfamily
A, C, E, G	IPR006162	Phosphopantetheine attachment site	PTM
A, C, E, G	IPR009081	Phosphopantetheine binding ACP domain	Domain
A, C, E, G	IPR036736	ACP-like superfamily	Homologous Superfamily
A, C, E, G	IPR003231	Acyl carrier protein	Family

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.