2WAD

PENICILLIN-BINDING PROTEIN 2B (PBP-2B) FROM STREPTOCOCCUS PNEUMONIAE (STRAIN 5204)

External Resource: Annotation

Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A	PBP_dimer	e2wadA6	A: beta complex topology	X: Penicillin binding protein dimerisation domain (From Topology)	H: Penicillin binding protein dimerisation domain (From Topology)	T: Penicillin binding protein dimerisation domain	F: PBP_dimer	ECOD (1.6)
A	Transpeptidase_1st_1	e2wadA7	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: Transpeptidase_1st_1	ECOD (1.6)
A	PBP_dimer_1	e2wadA4	A: a+b two layers	X: ClpS-like	H: Penicillin binding protein ClpS-like domain (From Topology)	T: Penicillin binding protein ClpS-like domain	F: PBP_dimer_1	ECOD (1.6)
A	Transpeptidase_2nd	e2wadA5	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: Transpeptidase_2nd	ECOD (1.6)
B	PBP_dimer	e2wadB6	A: beta complex topology	X: Penicillin binding protein dimerisation domain (From Topology)	H: Penicillin binding protein dimerisation domain (From Topology)	T: Penicillin binding protein dimerisation domain	F: PBP_dimer	ECOD (1.6)
B	Transpeptidase_1st_1	e2wadB7	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: Transpeptidase_1st_1	ECOD (1.6)
B	PBP_dimer_1	e2wadB4	A: a+b two layers	X: ClpS-like	H: Penicillin binding protein ClpS-like domain (From Topology)	T: Penicillin binding protein ClpS-like domain	F: PBP_dimer_1	ECOD (1.6)
B	Transpeptidase_2nd	e2wadB5	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: Transpeptidase_2nd	ECOD (1.6)
C	PBP_dimer	e2wadC1	A: beta complex topology	X: Penicillin binding protein dimerisation domain (From Topology)	H: Penicillin binding protein dimerisation domain (From Topology)	T: Penicillin binding protein dimerisation domain	F: PBP_dimer	ECOD (1.6)
C	Transpeptidase_1st_1	e2wadC2	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: Transpeptidase_1st_1	ECOD (1.6)
C	PBP_dimer_1	e2wadC3	A: a+b two layers	X: ClpS-like	H: Penicillin binding protein ClpS-like domain (From Topology)	T: Penicillin binding protein ClpS-like domain	F: PBP_dimer_1	ECOD (1.6)
C	Transpeptidase_2nd	e2wadC4	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: Transpeptidase_2nd	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	6.20.70.10	Special	Other non-globular	Ubiquitin Ligase Nedd4	Chain: W	CATH (4.3.0)
A	3.90.1310.10	Alpha Beta	Alpha-Beta Complex	Penicillin-binding protein 2a (Domain 2)	Penicillin-binding protein 2a (Domain 2)	CATH (4.3.0)
A	1.10.10.1230	Mainly Alpha	Orthogonal Bundle	Arc Repressor Mutant, subunit A	Penicillin-binding protein, N-terminal non-catalytic domain, head sub-domain	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)
B	6.20.70.10	Special	Other non-globular	Ubiquitin Ligase Nedd4	Chain: W	CATH (4.3.0)
B	3.90.1310.10	Alpha Beta	Alpha-Beta Complex	Penicillin-binding protein 2a (Domain 2)	Penicillin-binding protein 2a (Domain 2)	CATH (4.3.0)
B	1.10.10.1230	Mainly Alpha	Orthogonal Bundle	Arc Repressor Mutant, subunit A	Penicillin-binding protein, N-terminal non-catalytic domain, head sub-domain	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)
C	6.20.70.10	Special	Other non-globular	Ubiquitin Ligase Nedd4	Chain: W	CATH (4.3.0)
C	3.90.1310.10	Alpha Beta	Alpha-Beta Complex	Penicillin-binding protein 2a (Domain 2)	Penicillin-binding protein 2a (Domain 2)	CATH (4.3.0)
C	1.10.10.1230	Mainly Alpha	Orthogonal Bundle	Arc Repressor Mutant, subunit A	Penicillin-binding protein, N-terminal non-catalytic domain, head sub-domain	CATH (4.3.0)
C	3.40.710.10	Alpha Beta	3-Layer(aba) Sandwich	Beta-lactamase	DD-peptidase/beta-lactamase superfamily	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C	PF03717	Penicillin-binding Protein dimerisation domain (PBP_dimer)	Penicillin-binding Protein dimerisation domain	This domain is found at the N terminus of Class B High Molecular Weight Penicillin-Binding Proteins. Its function has not been precisely defined, but is strongly implicated in PBP polymerisation. The domain forms a largely disordered 'sugar tongs' st ...	This domain is found at the N terminus of Class B High Molecular Weight Penicillin-Binding Proteins. Its function has not been precisely defined, but is strongly implicated in PBP polymerisation. The domain forms a largely disordered 'sugar tongs' structure.	Domain
A, B, C	PF00905	Penicillin binding protein transpeptidase domain (Transpeptidase)	Penicillin binding protein transpeptidase domain	The active site serine (residue 337 in Swiss:P14677) is conserved in all members of this family.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C	PENICILLIN-BINDING PROTEIN 2B	serine-type exopeptidase activity peptidase activity catalytic activity, acting on a protein serine hydrolase activity hydrolase activity peptidoglycan L,D-transpeptidase activity serine-type carboxypeptidase activity serine-type peptidase activity exopeptidase activity catalytic activity carboxypeptidase activity amide binding organic acid binding binding serine-type exopeptidase activity peptidase activity catalytic activity, acting on a protein serine hydrolase activity hydrolase activity peptidoglycan L,D-transpeptidase activity serine-type carboxypeptidase activity serine-type peptidase activity exopeptidase activity catalytic activity carboxypeptidase activity amide binding organic acid binding binding ion binding organic cyclic compound binding anion binding penicillin binding carboxylic acid binding heterocyclic compound binding monocarboxylic acid binding small molecule binding sulfur compound binding	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 cellular biosynthetic process cell wall organization or biogenesis glycosaminoglycan metabolic 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 cellular biosynthetic process cell wall organization or biogenesis glycosaminoglycan metabolic process organonitrogen compound biosynthetic process carbohydrate derivative metabolic process cellular component biogenesis organic substance metabolic process peptidoglycan metabolic process organic substance biosynthetic process nitrogen compound metabolic process glycosaminoglycan biosynthetic process cellular component organization or biogenesis carbohydrate derivative biosynthetic process peptidoglycan-based cell wall biogenesis organonitrogen compound metabolic process cellular metabolic process macromolecule biosynthetic process peptidoglycan biosynthetic process cell wall biogenesis biosynthetic process cell wall macromolecule biosynthetic process aminoglycan metabolic process aminoglycan biosynthetic process cellular process metabolic process macromolecule metabolic process cellular component organization cell wall organization external encapsulating structure organization response to stimulus response to chemical response to antibiotic	cell periphery plasma membrane membrane cellular anatomical entity

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C	IPR012338	Beta-lactamase/transpeptidase-like	Homologous Superfamily
A, B, C	IPR047982	Penicillin-binding protein 2B	Family
A, B, C	IPR005311	Penicillin-binding protein, dimerisation domain	Domain
A, B, C	IPR001460	Penicillin-binding protein, transpeptidase	Domain
A, B, C	IPR036138	Penicillin-binding protein, dimerisation domain superfamily	Homologous Superfamily

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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 R01GM133198.