4DKI | pdb_00004dki

Structural Insights into the Anti- Methicillin-Resistant Staphylococcus aureus (MRSA) Activity of Ceftobiprole

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
AMR Gene: CARD Annotation
AMR Gene Family: CARD 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)
B	d4dkib1	Alpha and beta proteins (a+b)	Cystatin-like	NTF2-like	Penicillin binding protein 2a (PBP2A), N-terminal domain	Penicillin binding protein 2a (PBP2A), N-terminal domain	(Staphylococcus aureus subsp. aureus COL ) [TaxId: 93062 ],	SCOPe (2.08)
B	d4dkib2	Alpha and beta proteins (a+b)	Penicillin binding protein dimerisation domain	Penicillin binding protein dimerisation domain	Penicillin binding protein dimerisation domain	Penicillin binding protein 2a (PBP2A), middle domain	(Staphylococcus aureus subsp. aureus COL ) [TaxId: 93062 ],	SCOPe (2.08)
B	d4dkib3	Multi-domain proteins (alpha and beta)	beta-lactamase/transpeptidase-like	beta-lactamase/transpeptidase-like	beta-Lactamase/D-ala carboxypeptidase	Penicillin binding protein 2a (PBP2A), C-terminal domain	(Staphylococcus aureus subsp. aureus COL ) [TaxId: 93062 ],	SCOPe (2.08)
A	d4dkia1	Alpha and beta proteins (a+b)	Cystatin-like	NTF2-like	Penicillin binding protein 2a (PBP2A), N-terminal domain	Penicillin binding protein 2a (PBP2A), N-terminal domain	(Staphylococcus aureus subsp. aureus COL ) [TaxId: 93062 ],	SCOPe (2.08)
A	d4dkia2	Alpha and beta proteins (a+b)	Penicillin binding protein dimerisation domain	Penicillin binding protein dimerisation domain	Penicillin binding protein dimerisation domain	Penicillin binding protein 2a (PBP2A), middle domain	(Staphylococcus aureus subsp. aureus COL ) [TaxId: 93062 ],	SCOPe (2.08)
A	d4dkia3	Multi-domain proteins (alpha and beta)	beta-lactamase/transpeptidase-like	beta-lactamase/transpeptidase-like	beta-Lactamase/D-ala carboxypeptidase	Penicillin binding protein 2a (PBP2A), C-terminal domain	(Staphylococcus aureus subsp. aureus COL ) [TaxId: 93062 ],	SCOPe (2.08)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
B	Transpeptidase	e4dkiB1	A: a/b three-layered sandwiches	X: DEATH domain	H: 40S ribosomal protein S13 N-terminal domain	T: 40S ribosomal protein S13 N-terminal domain	F: Transpeptidase	ECOD (v294.1)
A	Transpeptidase	e4dkiA1	A: a/b three-layered sandwiches	X: DEATH domain	H: 40S ribosomal protein S13 N-terminal domain	T: 40S ribosomal protein S13 N-terminal domain	F: Transpeptidase	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
B	3.10.450.100	Alpha Beta	Roll	Nuclear Transport Factor 2	Chain: A,	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	3.30.1390.30	Alpha Beta	2-Layer Sandwich	Ribosomal Protein L30	Chain: A,	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)
A	3.10.450.100	Alpha Beta	Roll	Nuclear Transport Factor 2	Chain: A,	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	3.30.1390.30	Alpha Beta	2-Layer Sandwich	Ribosomal Protein L30	Chain: A,	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)

AMR Gene: CARD Annotation CARD Database Homepage

Chains	Accession	Short Name	Description	Provenance Source (Version)
A, B	ARO:3000617	mecA	A foreign PBP2a acquired by lateral gene transfer that is able to perform peptidoglycan synthesis in the presence of beta-lactams.	CARD (4.0.1)

AMR Gene Family: CARD Annotation CARD Database Homepage

Chains	Accession	Gene Family	Drug Class	Resistance Machanism	Provenance Source (Version)
A, B	ARO:3001208	methicillin resistant PBP2	penicillin beta-lactam	antibiotic target replacement	CARD (4.0.1)

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B	Penicillin-binding protein 2'	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 organic acid binding binding ion 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 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 D-Ala-D-Ala carboxypeptidase activity	cellular component organization cell wall organization or biogenesis cell wall organization cellular process cellular component organization or biogenesis external encapsulating structure organization response to stimulus response to chemical response to antibiotic	cell periphery cellular anatomical structure plasma membrane membrane

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR032710	NTF2-like domain superfamily	Homologous Superfamily
A, B	IPR012338	Beta-lactamase/transpeptidase-like	Homologous Superfamily
A, B	IPR007887	Penicillin-binding protein 3-like, N-terminal domain	Domain
A, B	IPR036138	Penicillin-binding protein, dimerisation domain superfamily	Homologous Superfamily
A, B	IPR005311	Penicillin-binding protein, dimerisation domain	Domain
A, B	IPR001460	Penicillin-binding protein, transpeptidase	Domain
A, B	IPR050515	Class D beta-lactamase/transpeptidase	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.