5ZQD | pdb_00005zqd

Crystal Structure of Penicillin-Binding Protein D2 from Listeria monocytogenes in the Cefotaxime bound form

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
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	d5zqda_	Multi-domain proteins (alpha and beta)	beta-lactamase/transpeptidase-like	beta-lactamase/transpeptidase-like	automated matches	automated matches	(Listeria monocytogenes EGD-e ) [TaxId: 169963 ],	SCOPe (2.08)
B	d5zqdb_	Multi-domain proteins (alpha and beta)	beta-lactamase/transpeptidase-like	beta-lactamase/transpeptidase-like	automated matches	automated matches	(Listeria monocytogenes EGD-e ) [TaxId: 169963 ],	SCOPe (2.08)
C	d5zqdc_	Multi-domain proteins (alpha and beta)	beta-lactamase/transpeptidase-like	beta-lactamase/transpeptidase-like	automated matches	automated matches	(Listeria monocytogenes EGD-e ) [TaxId: 169963 ],	SCOPe (2.08)
D	d5zqdd_	Multi-domain proteins (alpha and beta)	beta-lactamase/transpeptidase-like	beta-lactamase/transpeptidase-like	automated matches	automated matches	(Listeria monocytogenes EGD-e ) [TaxId: 169963 ],	SCOPe (2.08)
E	d5zqde_	Multi-domain proteins (alpha and beta)	beta-lactamase/transpeptidase-like	beta-lactamase/transpeptidase-like	automated matches	automated matches	(Listeria monocytogenes EGD-e ) [TaxId: 169963 ],	SCOPe (2.08)
F	d5zqdf_	Multi-domain proteins (alpha and beta)	beta-lactamase/transpeptidase-like	beta-lactamase/transpeptidase-like	automated matches	automated matches	(Listeria monocytogenes EGD-e ) [TaxId: 169963 ],	SCOPe (2.08)
G	d5zqdg_	Multi-domain proteins (alpha and beta)	beta-lactamase/transpeptidase-like	beta-lactamase/transpeptidase-like	automated matches	automated matches	(Listeria monocytogenes EGD-e ) [TaxId: 169963 ],	SCOPe (2.08)
H	d5zqdh_	Multi-domain proteins (alpha and beta)	beta-lactamase/transpeptidase-like	beta-lactamase/transpeptidase-like	automated matches	automated matches	(Listeria monocytogenes EGD-e ) [TaxId: 169963 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	beta-lactamase/transpeptidase-like	8080748	3001604	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	beta-lactamase/transpeptidase-like	8080748	3001604	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	beta-lactamase/transpeptidase-like	8080748	3001604	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	beta-lactamase/transpeptidase-like	8080748	3001604	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	beta-lactamase/transpeptidase-like	8080748	3001604	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	beta-lactamase/transpeptidase-like	8080748	3001604	SCOP2B (2022-06-29)
G	SCOP2B Superfamily	beta-lactamase/transpeptidase-like	8080748	3001604	SCOP2B (2022-06-29)
H	SCOP2B Superfamily	beta-lactamase/transpeptidase-like	8080748	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_S11_1st_1	e5zqdA2	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_S11_1st_1	ECOD (1.6)
A	Peptidase_S11_2nd	e5zqdA1	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_S11_2nd	ECOD (1.6)
B	Peptidase_S11_1st_1	e5zqdB2	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_S11_1st_1	ECOD (1.6)
B	Peptidase_S11_2nd	e5zqdB1	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_S11_2nd	ECOD (1.6)
C	Peptidase_S11_1st_1	e5zqdC2	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_S11_1st_1	ECOD (1.6)
C	Peptidase_S11_2nd	e5zqdC1	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_S11_2nd	ECOD (1.6)
D	Peptidase_S11_1st_1	e5zqdD1	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_S11_1st_1	ECOD (1.6)
D	Peptidase_S11_2nd	e5zqdD2	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_S11_2nd	ECOD (1.6)
E	Peptidase_S11_1st_1	e5zqdE2	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_S11_1st_1	ECOD (1.6)
E	Peptidase_S11_2nd	e5zqdE1	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_S11_2nd	ECOD (1.6)
F	Peptidase_S11_1st_1	e5zqdF1	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_S11_1st_1	ECOD (1.6)
F	Peptidase_S11_2nd	e5zqdF2	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_S11_2nd	ECOD (1.6)
G	Peptidase_S11_1st_1	e5zqdG2	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_S11_1st_1	ECOD (1.6)
G	Peptidase_S11_2nd	e5zqdG1	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_S11_2nd	ECOD (1.6)
H	Peptidase_S11_1st_1	e5zqdH2	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_S11_1st_1	ECOD (1.6)
H	Peptidase_S11_2nd	e5zqdH1	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_S11_2nd	ECOD (1.6)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D, E A, B, C, D, E, F, G, H	PF00144	Beta-lactamase (Beta-lactamase)	Beta-lactamase	This family appears to be distantly related to Pfam:PF00905 and PF00768 D-alanyl-D-alanine carboxypeptidase.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D, E A, B, C, D, E, F, G, H	Lmo2812 protein	serine-type exopeptidase activity peptidase activity catalytic activity, acting on a protein serine hydrolase activity hydrolase activity serine-type D-Ala-D-Ala carboxypeptidase activity serine-type carboxypeptidase activity serine-type peptidase activity exopeptidase activity catalytic activity carboxypeptidase activity cation binding ion binding binding serine-type exopeptidase activity peptidase activity catalytic activity, acting on a protein serine hydrolase activity hydrolase activity serine-type D-Ala-D-Ala carboxypeptidase activity serine-type carboxypeptidase activity serine-type peptidase activity exopeptidase activity catalytic activity carboxypeptidase activity cation binding ion binding binding metal ion binding small molecule 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 carbohydrate derivative biosynthetic process peptidoglycan-based cell wall biogenesis cell wall organization or biogenesis 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 carbohydrate derivative biosynthetic process peptidoglycan-based cell wall biogenesis cell wall organization or 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 cellular process metabolic process glycosaminoglycan biosynthetic process cellular component organization or biogenesis macromolecule metabolic process cell wall macromolecule metabolic process proteolysis primary metabolic process protein metabolic process cellular component organization cell wall organization external encapsulating structure organization	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D, E A, B, C, D, E, F, G, H	IPR018044	Peptidase S11, D-alanyl-D-alanine carboxypeptidase A	Family
A, B, C, D, E A, B, C, D, E, F, G, H	IPR012338	Beta-lactamase/transpeptidase-like	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F, G, H	IPR001967	Peptidase S11, D-alanyl-D-alanine carboxypeptidase A, N-terminal	Domain

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.