2EX9 | pdb_00002ex9

Crystal structure of penicillin binding protein 4 (dacB) from Escherichia coli, complexed with penicillin-V

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)
A	d2ex9a_	Multi-domain proteins (alpha and beta)	beta-lactamase/transpeptidase-like	beta-lactamase/transpeptidase-like	Dac-like	DD-carboxypeptidase DacB	(Escherichia coli ) [TaxId: 562 ],	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	8040260	3001604	SCOP2B (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A	e2ex9A1	A: C-terminal subdomain in Lon-related proteases catalytic domains	X: PABC(PABP) domain	H: PABC(PABP) domain	T: PABP	F:	ECOD (20:10:01)
A	e2ex9A2	A: C-terminal subdomain in Lon-related proteases catalytic domains	X: C-terminal subdomain in Lon-related proteases catalytic domains	H: C-terminal subdomain in Lon-related proteases catalytic domains	T: Propep_M14	F:	ECOD (20:10:01)
A	e2ex9A3	A: C-terminal subdomain in Lon-related proteases catalytic domains	X: C-terminal subdomain in Lon-related proteases catalytic domains	H: C-terminal subdomain in Lon-related proteases catalytic domains	T: tRNA-synt_2	F:	ECOD (20:10:01)
A	e2ex9A4	A: HTH	X: HTH	H: winged helix domain	T: EF-hand_1, EF-hand_7	F:	ECOD (20:10:01)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.40.710.10	Alpha Beta	3-Layer(aba) Sandwich	Beta-lactamase	DD-peptidase/beta-lactamase superfamily	CATH (4.3.0)
A	3.50.80.20	Alpha Beta	3-Layer(bba) Sandwich	D-tyrosyl-trna(Tyr) Deacylase	Chain: A	CATH (4.3.0)

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	Penicillin-binding protein 4	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 serine-type exopeptidase activity peptidase activity catalytic activity, acting on a protein serine hydrolase activity 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 serine-type exopeptidase activity peptidase activity catalytic activity, acting on a protein serine hydrolase activity serine-type carboxypeptidase activity serine-type peptidase activity hydrolase activity exopeptidase activity catalytic activity carboxypeptidase activity endopeptidase activity serine-type D-Ala-D-Ala carboxypeptidase activity serine-type endopeptidase 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 glycosaminoglycan metabolic process aminoglycan metabolic process peptidoglycan 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 glycosaminoglycan metabolic process aminoglycan metabolic process peptidoglycan metabolic process carbohydrate derivative metabolic process metabolic process cellular process macromolecule metabolic process cellular component organization cell wall organization or biogenesis cell wall organization cellular component organization or biogenesis external encapsulating structure organization reproductive process in single-celled organism reproductive process cytokinesis cell division cell cycle FtsZ-dependent cytokinesis cell cycle process asexual reproduction response to stimulus response to chemical response to antibiotic carbohydrate derivative biosynthetic process peptidoglycan-based cell wall biogenesis macromolecule biosynthetic process cellular component biogenesis peptidoglycan biosynthetic process cell wall biogenesis biosynthetic process cell wall macromolecule biosynthetic process aminoglycan biosynthetic process glycosaminoglycan biosynthetic process cell wall macromolecule metabolic process proteolysis primary metabolic process protein metabolic process	cell periphery cellular anatomical structure plasma membrane membrane periplasmic space

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR012338	Beta-lactamase/transpeptidase-like	Homologous Superfamily
A	IPR000667	Peptidase S13, D-Ala-D-Ala carboxypeptidase C	Family

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.

Prepare Data

Validate Data

Deposit Data

Help and Resources

.id_divider{ color: #ccc; padding: 0 10px 0 10px; } .extended_id_info{ color: #ccc; font-size: 18px; position: relative; top: -10px; left: 4px; } 2EX9 | pdb_00002ex9