1TVF | pdb_00001tvf

Crystal Structure of penicillin-binding protein 4 (PBP4) from Staphylococcus aureus

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)
B	d1tvfb1	All beta proteins	Penicillin-binding protein associated domain	Penicillin-binding protein associated domain	Pencillin binding protein 4 (PbpD), C-terminal domain	Pencillin binding protein 4 (PbpD), C-terminal domain	(Staphylococcus aureus ) [TaxId: 1280 ],	SCOPe (2.08)
B	d1tvfb2	Multi-domain proteins (alpha and beta)	beta-lactamase/transpeptidase-like	beta-lactamase/transpeptidase-like	beta-Lactamase/D-ala carboxypeptidase	Pencillin binding protein 4 (PbpD), N-terminal domain	(Staphylococcus aureus ) [TaxId: 1280 ],	SCOPe (2.08)
B	d1tvfb3	Artifacts	Tags	Tags	Tags	N-terminal Tags	(Staphylococcus aureus ) [TaxId: 1280 ],	SCOPe (2.08)
A	d1tvfa1	All beta proteins	Penicillin-binding protein associated domain	Penicillin-binding protein associated domain	Pencillin binding protein 4 (PbpD), C-terminal domain	Pencillin binding protein 4 (PbpD), C-terminal domain	(Staphylococcus aureus ) [TaxId: 1280 ],	SCOPe (2.08)
A	d1tvfa2	Multi-domain proteins (alpha and beta)	beta-lactamase/transpeptidase-like	beta-lactamase/transpeptidase-like	beta-Lactamase/D-ala carboxypeptidase	Pencillin binding protein 4 (PbpD), N-terminal domain	(Staphylococcus aureus ) [TaxId: 1280 ],	SCOPe (2.08)
A	d1tvfa3	Artifacts	Tags	Tags	Tags	N-terminal Tags	(Staphylococcus aureus ) [TaxId: 1280 ],	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	8040466	3001604	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Penicillin-binding protein associated domain	8040465	3002006	SCOP2B (2022-06-29)
A	SCOP2 Family	Pencillin binding protein 4 (PbpD), C-terminal domain	8028086	4001701	SCOP2 (2022-06-29)
A	SCOP2 Family	beta-Lactamase/D-ala carboxypeptidase	8028087	4002685	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Penicillin-binding protein associated domain	8040465	3002006	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	beta-lactamase/transpeptidase-like	8040466	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	Ricin_B_lectin, RicinB_lectin_2	e1tvfB1	A: a/b three-layered sandwiches	X: Phage tail fiber protein trimerization domain	H: beta-Prism I	T: beta-Prism I	F: Ricin_B_lectin, RicinB_lectin_2	ECOD (v294.1)
B	Ion_trans_2	e1tvfB2	A: a/b three-layered sandwiches	X: ETN0001 domain-like	H: Rpp14/Pop5-like	T: Rpp14/Pop5-like	F: Ion_trans_2	ECOD (v294.1)
B	Transpeptidase	e1tvfB3	A: a/b three-layered sandwiches	X: ETN0001 domain-like	H: ETN0001 domain-like	T: Mss4-like	F: Transpeptidase	ECOD (v294.1)
A	DUF1958	e1tvfA1	A: beta sandwiches	X: Penicillin-binding protein associated domain	H: Penicillin-binding protein associated domain	T: Penicillin-binding protein associated domain	F: DUF1958	ECOD (v294.1)
A	Beta-lactamase	e1tvfA2	A: a+b two layers	X: alpha-helical domain in beta-lactamase/transpeptidase-like proteins	H: alpha-helical domain in beta-lactamase/transpeptidase-like proteins	T: alpha-helical domain in beta-lactamase/transpeptidase-like proteins	F: Beta-lactamase	ECOD (v294.1)
A	Transpeptidase	e1tvfA3	A: a+b three layers	X: Profilin-like	H: a+b domain in beta-lactamase/transpeptidase-like proteins	T: a+b domain in beta-lactamase/transpeptidase-like proteins	F: Transpeptidase	ECOD (v294.1)

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	2.30.140.20	Mainly Beta	Roll	Spermidine Synthase	Chain: A, domain 2	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	2.30.140.20	Mainly Beta	Roll	Spermidine Synthase	Chain: A, domain 2	CATH (4.3.0)

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B	penicillin binding protein 4	beta-lactamase activity hydrolase activity hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in cyclic amides catalytic activity hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds serine-type exopeptidase activity peptidase activity catalytic activity, acting on a protein serine hydrolase activity serine-type D-Ala-D-Ala carboxypeptidase activity serine-type carboxypeptidase activity serine-type peptidase activity exopeptidase activity carboxypeptidase activity	developmental process regulation of biological process regulation of developmental process biological regulation regulation of cell shape cell morphogenesis regulation of cell morphogenesis anatomical structure morphogenesis anatomical structure development regulation of biological quality regulation of anatomical structure morphogenesis antibiotic metabolic process beta-lactam antibiotic catabolic process catabolic process developmental process regulation of biological process regulation of developmental process biological regulation regulation of cell shape cell morphogenesis regulation of cell morphogenesis anatomical structure morphogenesis anatomical structure development regulation of biological quality regulation of anatomical structure morphogenesis antibiotic metabolic process beta-lactam antibiotic catabolic process catabolic process lactam catabolic process metabolic process cellular process small molecule metabolic process antibiotic catabolic process lactam metabolic process cellular component organization cell wall organization or biogenesis cell wall organization cellular component organization or biogenesis external encapsulating structure organization response to stimulus response to chemical response to antibiotic carbohydrate derivative biosynthetic process peptidoglycan-based cell wall biogenesis glycosaminoglycan metabolic process carbohydrate derivative metabolic process macromolecule biosynthetic process cellular component biogenesis peptidoglycan biosynthetic process cell wall biogenesis biosynthetic process cell wall macromolecule biosynthetic process aminoglycan metabolic process peptidoglycan metabolic process aminoglycan biosynthetic process glycosaminoglycan biosynthetic process macromolecule metabolic process cell wall macromolecule metabolic process proteolysis primary metabolic process protein metabolic process	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR015294	Penicillin-binding protein 4, C-terminal domain	Domain
A, B	IPR018044	Peptidase S11, D-alanyl-D-alanine carboxypeptidase A	Family
A, B	IPR012338	Beta-lactamase/transpeptidase-like	Homologous Superfamily
A, B	IPR015956	Penicillin-binding protein, C-terminal domain superfamily	Homologous Superfamily
A, B	IPR000871	Beta-lactamase, class-A	Family
A, B	IPR001967	Peptidase S11, D-alanyl-D-alanine carboxypeptidase A, N-terminal	Domain
A, B	IPR037091	Penicillin-binding protein 4, C-terminal domain 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.