2NXO | pdb_00002nxo

Crystal structure of protein SCO4506 from Streptomyces coelicolor, Pfam DUF178

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	d2nxod_	Alpha and beta proteins (a/b)	Periplasmic binding protein-like II	Periplasmic binding protein-like II	Phosphate binding protein-like	Hypothetical protein SCo4506	(Streptomyces coelicolor ) [TaxId: 1902 ],	SCOPe (2.08)
C	d2nxoc_	Alpha and beta proteins (a/b)	Periplasmic binding protein-like II	Periplasmic binding protein-like II	Phosphate binding protein-like	Hypothetical protein SCo4506	(Streptomyces coelicolor ) [TaxId: 1902 ],	SCOPe (2.08)
B	d2nxob_	Alpha and beta proteins (a/b)	Periplasmic binding protein-like II	Periplasmic binding protein-like II	Phosphate binding protein-like	Hypothetical protein SCo4506	(Streptomyces coelicolor ) [TaxId: 1902 ],	SCOPe (2.08)
A	d2nxoa1	Alpha and beta proteins (a/b)	Periplasmic binding protein-like II	Periplasmic binding protein-like II	Phosphate binding protein-like	Hypothetical protein SCo4506	(Streptomyces coelicolor ) [TaxId: 1902 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
D	SCOP2B Superfamily	Type 2 solute binding protein-like	8034914	3000083	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Type 2 solute binding protein-like	8034914	3000083	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Type 2 solute binding protein-like	8034914	3000083	SCOP2B (2022-06-29)
A	SCOP2 Family	Phosphate binding protein-like	8022534	4000229	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Type 2 solute binding protein-like	8034914	3000083	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	LysR_substrate	e2nxoD1	A: alpha bundles	X: Rossmann-like	H: Glycosyl hydrolase domain	T: Glycosyl hydrolase domain	F: LysR_substrate	ECOD (develop294)
C	LysR_substrate	e2nxoC1	A: alpha bundles	X: Rossmann-like	H: Glycosyl hydrolase domain	T: Glycosyl hydrolase domain	F: LysR_substrate	ECOD (develop294)
B	LysR_substrate	e2nxoB1	A: alpha bundles	X: Rossmann-like	H: Glycosyl hydrolase domain	T: Glycosyl hydrolase domain	F: LysR_substrate	ECOD (develop294)
A	SBP_bac_11	e2nxoA2	A: alpha bundles	X: Alpha-beta plaits	H: Protease propeptides/inhibitors	T: Protease propeptides/inhibitors	F: SBP_bac_11	ECOD (develop294)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
D	3.40.190.10	Alpha Beta	3-Layer(aba) Sandwich	D-Maltodextrin-Binding Protein	domain 2	CATH (4.3.0)
C	3.40.190.10	Alpha Beta	3-Layer(aba) Sandwich	D-Maltodextrin-Binding Protein	domain 2	CATH (4.3.0)
B	3.40.190.10	Alpha Beta	3-Layer(aba) Sandwich	D-Maltodextrin-Binding Protein	domain 2	CATH (4.3.0)
A	3.40.190.10	Alpha Beta	3-Layer(aba) Sandwich	D-Maltodextrin-Binding Protein	domain 2	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D	PF02621	Menaquinone biosynthesis (VitK2_biosynth)	Menaquinone biosynthesis	This family includes two enzymes which are involved in menaquinone biosynthesis. One which catalyses the conversion of cyclic de-hypoxanthine futalosine to 1,4-dihydroxy-6-naphthoate, and one which may be involved in the conversion of chorismate to f ...	This family includes two enzymes which are involved in menaquinone biosynthesis. One which catalyses the conversion of cyclic de-hypoxanthine futalosine to 1,4-dihydroxy-6-naphthoate, and one which may be involved in the conversion of chorismate to futalosine [1]. These enzymes comprise two domains with alpha/beta structures, a large domain and a small domain. A pocket between the two domains may form the active site, a conserved histidine located within this pocket could be the catalytic base [2].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D	Hypothetical protein SCO4506	hydro-lyase activity lyase activity catalytic activity carbon-oxygen lyase activity	biosynthetic process small molecule biosynthetic process ketone metabolic process menaquinone metabolic process metabolic process cellular process small molecule metabolic process menaquinone biosynthetic process ketone biosynthetic process	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D	IPR030868	Chorismate dehydratase	Family
A, B, C, D	IPR003773	Menaquinone biosynthesis enzyme	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.