3A3E

Crystal structure of penicillin binding protein 4 (dacB) from Haemophilus influenzae, complexed with novel beta-lactam (CMV)

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)
B	d3a3eb1	Multi-domain proteins (alpha and beta)	beta-lactamase/transpeptidase-like	beta-lactamase/transpeptidase-like	Dac-like	DD-carboxypeptidase DacB	(Haemophilus influenzae ) [TaxId: 727 ],	SCOPe (2.08)
B	d3a3eb2	Artifacts	Tags	Tags	Tags	N-terminal Tags	(Haemophilus influenzae ) [TaxId: 727 ],	SCOPe (2.08)
A	d3a3ea1	Multi-domain proteins (alpha and beta)	beta-lactamase/transpeptidase-like	beta-lactamase/transpeptidase-like	Dac-like	DD-carboxypeptidase DacB	(Haemophilus influenzae ) [TaxId: 727 ],	SCOPe (2.08)
A	d3a3ea2	Artifacts	Tags	Tags	Tags	N-terminal Tags	(Haemophilus influenzae ) [TaxId: 727 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
B	SCOP2B Superfamily	beta-lactamase/transpeptidase-like	8079023	3001604	SCOP2B (2022-06-29)
A	SCOP2 Family	Dac-like	8079022	4000441	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	beta-lactamase/transpeptidase-like	8079023	3001604	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)
B	Peptidase_S13_1st,Peptidase_S13_2nd	e3a3eB1	A: beta complex topology	X: Inserted beta sandwich domain in Dac-like proteins (From Topology)	H: Inserted beta sandwich domain in Dac-like proteins (From Topology)	T: Inserted beta sandwich domain in Dac-like proteins	F: Peptidase_S13_1st,Peptidase_S13_2nd	ECOD (1.6)
B	Peptidase_S13_3rd	e3a3eB4	A: alpha complex topology	X: alpha-helical domain in beta-lactamase/transpeptidase-like proteins (From Topology)	H: alpha-helical domain in beta-lactamase/transpeptidase-like proteins (From Topology)	T: alpha-helical domain in beta-lactamase/transpeptidase-like proteins	F: Peptidase_S13_3rd	ECOD (1.6)
B	Peptidase_S13_4th	e3a3eB3	A: a+b three layers	X: Profilin-like	H: a+b domain in beta-lactamase/transpeptidase-like proteins (From Topology)	T: a+b domain in beta-lactamase/transpeptidase-like proteins	F: Peptidase_S13_4th	ECOD (1.6)
B	Peptidase_S13_1st	e3a3eB2	A: a/b three-layered sandwiches	X: DTD-like	H: Inserted a+b domain in Dac-like proteins (From Topology)	T: Inserted a+b domain in Dac-like proteins	F: Peptidase_S13_1st	ECOD (1.6)
A	Peptidase_S13_2nd	e3a3eA8	A: beta complex topology	X: Inserted beta sandwich domain in Dac-like proteins (From Topology)	H: Inserted beta sandwich domain in Dac-like proteins (From Topology)	T: Inserted beta sandwich domain in Dac-like proteins	F: Peptidase_S13_2nd	ECOD (1.6)
A	Peptidase_S13_3rd	e3a3eA6	A: alpha complex topology	X: alpha-helical domain in beta-lactamase/transpeptidase-like proteins (From Topology)	H: alpha-helical domain in beta-lactamase/transpeptidase-like proteins (From Topology)	T: alpha-helical domain in beta-lactamase/transpeptidase-like proteins	F: Peptidase_S13_3rd	ECOD (1.6)
A	Peptidase_S13_4th	e3a3eA5	A: a+b three layers	X: Profilin-like	H: a+b domain in beta-lactamase/transpeptidase-like proteins (From Topology)	T: a+b domain in beta-lactamase/transpeptidase-like proteins	F: Peptidase_S13_4th	ECOD (1.6)
A	Peptidase_S13_1st	e3a3eA7	A: a/b three-layered sandwiches	X: DTD-like	H: Inserted a+b domain in Dac-like proteins (From Topology)	T: Inserted a+b domain in Dac-like proteins	F: Peptidase_S13_1st	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
B	3.40.710.10	Alpha Beta	3-Layer(aba) Sandwich	Beta-lactamase	DD-peptidase/beta-lactamase superfamily	CATH (4.3.0)
B	3.50.80.20	Alpha Beta	3-Layer(bba) Sandwich	D-tyrosyl-trna(Tyr) Deacylase	Chain: A	CATH (4.3.0)
A	3.40.710.10	Alpha Beta	3-Layer(aba) Sandwich	Beta-lactamase	DD-peptidase/beta-lactamase superfamily	CATH (4.3.0)
A	3.50.80.20	Alpha Beta	3-Layer(bba) Sandwich	D-tyrosyl-trna(Tyr) Deacylase	Chain: A	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B	PF02113	D-Ala-D-Ala carboxypeptidase 3 (S13) family (Peptidase_S13)	D-Ala-D-Ala carboxypeptidase 3 (S13) family	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B	Penicillin-binding protein 4	serine-type exopeptidase activity peptidase activity catalytic activity, acting on a protein serine hydrolase activity serine-type carboxypeptidase activity serine-type peptidase activity hydrolase activity exopeptidase activity catalytic activity carboxypeptidase activity	glycosaminoglycan metabolic process aminoglycan metabolic process peptidoglycan metabolic process carbohydrate derivative metabolic process metabolic process cellular process macromolecule metabolic process proteolysis primary metabolic process protein metabolic process	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR012338	Beta-lactamase/transpeptidase-like	Homologous Superfamily
A, B	IPR000667	Peptidase S13, D-Ala-D-Ala carboxypeptidase C	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.