2ZC3 | pdb_00002zc3

Penicillin-binding protein 2X (PBP 2X) acyl-enzyme complex (biapenem) from Streptococcus pneumoniae

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)
C	d2zc3c1	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)
F	d2zc3f1	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	d2zc3b_	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)
E	d2zc3e_	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: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
C	SCOP2B Superfamily	Penicillin-binding protein 2x (pbp-2x), c-terminal domain	8034366	3000202	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Penicillin-binding protein 2x (pbp-2x), c-terminal domain	8034369	3000202	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	Penicillin-binding protein 2x (pbp-2x), c-terminal domain	8034369	3000202	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	Penicillin-binding protein 2x (pbp-2x), c-terminal domain	8034366	3000202	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	beta-lactamase/transpeptidase-like	8037377	3001604	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	beta-lactamase/transpeptidase-like	8037377	3001604	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Penicillin binding protein dimerisation domain	8037247	3001420	SCOP2B (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
C	e2zc3C1	A: Suppressor of Fused, C-terminal domain	X: HTH	H: winged helix domain	T: GPW_gp25	F:	ECOD (20:10:01)
F	e2zc3F1	A: Suppressor of Fused, C-terminal domain	X: HTH	H: winged helix domain	T: GPW_gp25	F:	ECOD (20:10:01)
B	e2zc3B1	A: Nat/Ivy	X: Acyl-CoA N-acyltransferases (Nat)	H: Acyl-CoA N-acyltransferases (Nat)	T: MoCoBD_2	F:	ECOD (20:10:01)
E	e2zc3E1	A: Nat/Ivy	X: Acyl-CoA N-acyltransferases (Nat)	H: Acyl-CoA N-acyltransferases (Nat)	T: MoCoBD_2	F:	ECOD (20:10:01)
A	e2zc3A1	A: Nat/Ivy	X: Acyl-CoA N-acyltransferases (Nat)	H: Acyl-CoA N-acyltransferases (Nat)	T: MoCoBD_2	F:	ECOD (20:10:01)
D	e2zc3D1	A: amino-terminal domain of OmpATb	X: amino-terminal domain of OmpATb	H: amino-terminal domain of OmpATb	T: Internalin_N	F:	ECOD (20:10:01)

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)
E	3.40.710.10	Alpha Beta	3-Layer(aba) Sandwich	Beta-lactamase	DD-peptidase/beta-lactamase superfamily	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	3.30.70.2110	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits		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	3.30.70.2110	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits		CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
C, F	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
B, E	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
C, F	Penicillin-binding protein 2X	organic acid binding binding ion 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 process cell division cellular component organization 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 process cell division 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 metabolic process glycosaminoglycan biosynthetic process macromolecule metabolic process cell wall macromolecule metabolic process	cell periphery cellular anatomical structure plasma membrane membrane
B, E	Penicillin-binding protein 2X	organic acid binding binding ion 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 process cell division cellular component organization 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 process cell division 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 metabolic process glycosaminoglycan biosynthetic process macromolecule metabolic process cell wall macromolecule metabolic process	cell periphery cellular anatomical structure plasma membrane membrane
A, D	Penicillin-binding protein 2X	organic acid binding binding ion 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 process cell division cellular component organization 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 process cell division 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 metabolic process glycosaminoglycan biosynthetic process macromolecule metabolic process cell wall macromolecule metabolic process	cell periphery cellular anatomical structure plasma membrane membrane

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
C, F	IPR012338	Beta-lactamase/transpeptidase-like	Homologous Superfamily
C, F	IPR036138	Penicillin-binding protein, dimerisation domain superfamily	Homologous Superfamily
C, F	IPR053467	Penicillin-binding protein 2x	Family
C, F	IPR005543	PASTA domain	Domain
C, F	IPR005311	Penicillin-binding protein, dimerisation domain	Domain
C, F	IPR001460	Penicillin-binding protein, transpeptidase	Domain
C, F	IPR050515	Class D beta-lactamase/transpeptidase	Family
B, E	IPR012338	Beta-lactamase/transpeptidase-like	Homologous Superfamily
B, E	IPR036138	Penicillin-binding protein, dimerisation domain superfamily	Homologous Superfamily
B, E	IPR053467	Penicillin-binding protein 2x	Family
B, E	IPR005543	PASTA domain	Domain
B, E	IPR005311	Penicillin-binding protein, dimerisation domain	Domain
B, E	IPR001460	Penicillin-binding protein, transpeptidase	Domain
B, E	IPR050515	Class D beta-lactamase/transpeptidase	Family
A, D	IPR012338	Beta-lactamase/transpeptidase-like	Homologous Superfamily
A, D	IPR036138	Penicillin-binding protein, dimerisation domain superfamily	Homologous Superfamily
A, D	IPR053467	Penicillin-binding protein 2x	Family
A, D	IPR005543	PASTA domain	Domain
A, D	IPR005311	Penicillin-binding protein, dimerisation domain	Domain
A, D	IPR001460	Penicillin-binding protein, transpeptidase	Domain
A, D	IPR050515	Class D beta-lactamase/transpeptidase	Family