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)
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)
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)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2 Family	Dac-like	8079022	4000441	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	beta-lactamase/transpeptidase-like	8079023	3001604	SCOP2 (2022-06-29)
B	SCOP2B Superfamily	beta-lactamase/transpeptidase-like	8079023	3001604	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	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)
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)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
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)
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)

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	proteolysis metabolic process cellular process primary metabolic process protein metabolic process macromolecule 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.