1K25

PBP2x from a Highly Penicillin-resistant Streptococcus pneumoniae Clinical Isolate

External Resource: Annotation

Domain Annotation: SCOP/SCOPe 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	d1k25a1	Alpha and beta proteins (a+b)	Penicillin-binding protein 2x (pbp-2x), c-terminal domain	Penicillin-binding protein 2x (pbp-2x), c-terminal domain	Penicillin-binding protein 2x (pbp-2x), c-terminal domain	Penicillin-binding protein 2x (pbp-2x), c-terminal domain	(Streptococcus pneumoniae ) [TaxId: 1313 ],	SCOPe (2.08)
A	d1k25a3	Alpha and beta proteins (a+b)	Penicillin binding protein dimerisation domain	Penicillin binding protein dimerisation domain	Penicillin binding protein dimerisation domain	Penicillin-binding protein 2x (pbp-2x), N-terminal domain	(Streptococcus pneumoniae ) [TaxId: 1313 ],	SCOPe (2.08)
A	d1k25a4	Multi-domain proteins (alpha and beta)	beta-lactamase/transpeptidase-like	beta-lactamase/transpeptidase-like	beta-Lactamase/D-ala carboxypeptidase	Penicillin-binding protein 2x (pbp-2x), transpeptidase domain	(Streptococcus pneumoniae ) [TaxId: 1313 ],	SCOPe (2.08)
C	d1k25c1	Alpha and beta proteins (a+b)	Penicillin-binding protein 2x (pbp-2x), c-terminal domain	Penicillin-binding protein 2x (pbp-2x), c-terminal domain	Penicillin-binding protein 2x (pbp-2x), c-terminal domain	Penicillin-binding protein 2x (pbp-2x), c-terminal domain	(Streptococcus pneumoniae ) [TaxId: 1313 ],	SCOPe (2.08)
C	d1k25c3	Alpha and beta proteins (a+b)	Penicillin binding protein dimerisation domain	Penicillin binding protein dimerisation domain	Penicillin binding protein dimerisation domain	Penicillin-binding protein 2x (pbp-2x), N-terminal domain	(Streptococcus pneumoniae ) [TaxId: 1313 ],	SCOPe (2.08)
C	d1k25c4	Multi-domain proteins (alpha and beta)	beta-lactamase/transpeptidase-like	beta-lactamase/transpeptidase-like	beta-Lactamase/D-ala carboxypeptidase	Penicillin-binding protein 2x (pbp-2x), transpeptidase domain	(Streptococcus pneumoniae ) [TaxId: 1313 ],	SCOPe (2.08)
B	d1k25b1	Alpha and beta proteins (a+b)	Penicillin-binding protein 2x (pbp-2x), c-terminal domain	Penicillin-binding protein 2x (pbp-2x), c-terminal domain	Penicillin-binding protein 2x (pbp-2x), c-terminal domain	Penicillin-binding protein 2x (pbp-2x), c-terminal domain	(Streptococcus pneumoniae ) [TaxId: 1313 ],	SCOPe (2.08)
B	d1k25b3	Alpha and beta proteins (a+b)	Penicillin binding protein dimerisation domain	Penicillin binding protein dimerisation domain	Penicillin binding protein dimerisation domain	Penicillin-binding protein 2x (pbp-2x), N-terminal domain	(Streptococcus pneumoniae ) [TaxId: 1313 ],	SCOPe (2.08)
B	d1k25b4	Multi-domain proteins (alpha and beta)	beta-lactamase/transpeptidase-like	beta-lactamase/transpeptidase-like	beta-Lactamase/D-ala carboxypeptidase	Penicillin-binding protein 2x (pbp-2x), transpeptidase domain	(Streptococcus pneumoniae ) [TaxId: 1313 ],	SCOPe (2.08)
D	d1k25d1	Alpha and beta proteins (a+b)	Penicillin-binding protein 2x (pbp-2x), c-terminal domain	Penicillin-binding protein 2x (pbp-2x), c-terminal domain	Penicillin-binding protein 2x (pbp-2x), c-terminal domain	Penicillin-binding protein 2x (pbp-2x), c-terminal domain	(Streptococcus pneumoniae ) [TaxId: 1313 ],	SCOPe (2.08)
D	d1k25d3	Alpha and beta proteins (a+b)	Penicillin binding protein dimerisation domain	Penicillin binding protein dimerisation domain	Penicillin binding protein dimerisation domain	Penicillin-binding protein 2x (pbp-2x), N-terminal domain	(Streptococcus pneumoniae ) [TaxId: 1313 ],	SCOPe (2.08)
D	d1k25d4	Multi-domain proteins (alpha and beta)	beta-lactamase/transpeptidase-like	beta-lactamase/transpeptidase-like	beta-Lactamase/D-ala carboxypeptidase	Penicillin-binding protein 2x (pbp-2x), transpeptidase domain	(Streptococcus pneumoniae ) [TaxId: 1313 ],	SCOPe (2.08)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A	PF03717	e1k25A1	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: PF03717	ECOD (1.6)
A	PF00905	e1k25A3	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: PF00905	ECOD (1.6)
A	PF03793	e1k25A5	A: a+b two layers	X: CI-2 family of serine protease inhibitors-like	H: Penicillin-binding protein 2x (pbp-2x)-C (From Topology)	T: Penicillin-binding protein 2x (pbp-2x)-C	F: PF03793	ECOD (1.6)
A	PF00905	e1k25A2	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: PF00905	ECOD (1.6)
C	PF03717	e1k25C8	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: PF03717	ECOD (1.6)
C	PF00905	e1k25C9	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: PF00905	ECOD (1.6)
C	PF03793	e1k25C11	A: a+b two layers	X: CI-2 family of serine protease inhibitors-like	H: Penicillin-binding protein 2x (pbp-2x)-C (From Topology)	T: Penicillin-binding protein 2x (pbp-2x)-C	F: PF03793	ECOD (1.6)
C	PF00905	e1k25C12	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: PF00905	ECOD (1.6)
B	PF03717	e1k25B1	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: PF03717	ECOD (1.6)
B	PF00905	e1k25B2	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: PF00905	ECOD (1.6)
B	PF03793	e1k25B4	A: a+b two layers	X: CI-2 family of serine protease inhibitors-like	H: Penicillin-binding protein 2x (pbp-2x)-C (From Topology)	T: Penicillin-binding protein 2x (pbp-2x)-C	F: PF03793	ECOD (1.6)
B	F_UNCLASSIFIED	e1k25B3	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: F_UNCLASSIFIED	ECOD (1.6)
B	PF00905	e1k25B6	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: PF00905	ECOD (1.6)
D	PF03717	e1k25D1	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: PF03717	ECOD (1.6)
D	PF00905	e1k25D6	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: PF00905	ECOD (1.6)
D	PF03793	e1k25D5	A: a+b two layers	X: CI-2 family of serine protease inhibitors-like	H: Penicillin-binding protein 2x (pbp-2x)-C (From Topology)	T: Penicillin-binding protein 2x (pbp-2x)-C	F: PF03793	ECOD (1.6)
D	F_UNCLASSIFIED	e1k25D2	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: F_UNCLASSIFIED	ECOD (1.6)
D	PF00905	e1k25D4	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: PF00905	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
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	3.40.710.10	Alpha Beta	3-Layer(aba) Sandwich	Beta-lactamase	DD-peptidase/beta-lactamase superfamily	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	3.40.710.10	Alpha Beta	3-Layer(aba) Sandwich	Beta-lactamase	DD-peptidase/beta-lactamase superfamily	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	3.40.710.10	Alpha Beta	3-Layer(aba) Sandwich	Beta-lactamase	DD-peptidase/beta-lactamase superfamily	CATH (4.3.0)
D	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)
D	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, D	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, D	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
A, B, C, D	PF03793	PASTA domain (PASTA)	PASTA domain	This domain is found at the C termini of several Penicillin-binding proteins and bacterial serine/threonine kinases [1]. It binds the beta-lactam stem, which implicates it in sensing D-alanyl-D-alanine - the PBP transpeptidase substrate. It is a smal ...	This domain is found at the C termini of several Penicillin-binding proteins and bacterial serine/threonine kinases [1]. It binds the beta-lactam stem, which implicates it in sensing D-alanyl-D-alanine - the PBP transpeptidase substrate. It is a small globular fold consisting of 3 beta-sheets and an alpha-helix. The name PASTA is derived from PBP and Serine/Threonine kinase Associated domain.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D	low-affinity PENICILLIN-BINDING PROTEIN 2X	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	cell periphery plasma membrane membrane cellular anatomical entity

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D	IPR005543	PASTA domain	Domain
A, B, C, D	IPR012338	Beta-lactamase/transpeptidase-like	Homologous Superfamily
A, B, C, D	IPR005311	Penicillin-binding protein, dimerisation domain	Domain
A, B, C, D	IPR001460	Penicillin-binding protein, transpeptidase	Domain
A, B, C, D	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.