1VQQ | pdb_00001vqq

Structure of Penicillin binding protein 2a from methicillin resistant Staphylococcus aureus strain 27r at 1.80 A resolution.

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 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	d1vqqb1	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 ) [TaxId: 1280 ],	SCOPe (2.08)
B	d1vqqb2	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 ) [TaxId: 1280 ],	SCOPe (2.08)
B	d1vqqb3	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 ) [TaxId: 1280 ],	SCOPe (2.08)
A	d1vqqa1	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 ) [TaxId: 1280 ],	SCOPe (2.08)
A	d1vqqa2	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 ) [TaxId: 1280 ],	SCOPe (2.08)
A	d1vqqa3	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 ) [TaxId: 1280 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
B	SCOP2B Superfamily	Penicillin binding protein dimerisation domain	8043170	3001420	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	NTF2-like	8043169	3000472	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	beta-lactamase/transpeptidase-like	8043171	3001604	SCOP2B (2022-06-29)
A	SCOP2 Family	Penicillin binding protein 2a (PBP2A), N-terminal domain	8030790	4003182	SCOP2 (2022-06-29)
A	SCOP2 Family	Penicillin binding protein dimerisation domain	8030791	4002565	SCOP2 (2022-06-29)
A	SCOP2 Family	beta-Lactamase/D-ala carboxypeptidase	8030792	4002685	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	NTF2-like	8043169	3000472	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Penicillin binding protein dimerisation domain	8043170	3001420	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	beta-lactamase/transpeptidase-like	8043171	3001604	SCOP2 (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
B		e1vqqB1	A: alpha bundles	X: Thioredoxin-like	H: Thioredoxin-like	T: Thioredoxin-like	F:	ECOD (develop294)
A	Beta-lactamase	e1vqqA1	A: a+b two layers	X: alpha-helical domain in beta-lactamase/transpeptidase-like proteins	H: alpha-helical domain in beta-lactamase/transpeptidase-like proteins	T: alpha-helical domain in beta-lactamase/transpeptidase-like proteins	F: Beta-lactamase	ECOD (develop294)
A	SnoaL_2	e1vqqA3	A: a+b two layers	X: Cystatin-like	H: NTF2-like	T: NTF2-like	F: SnoaL_2	ECOD (develop294)
A	Transpeptidase	e1vqqA4	A: a+b three layers	X: Profilin-like	H: a+b domain in beta-lactamase/transpeptidase-like proteins	T: a+b domain in beta-lactamase/transpeptidase-like proteins	F: Transpeptidase	ECOD (develop294)
A	PBP_dimer	e1vqqA5	A: alpha bundles	X: jelly-roll	H: Zn-dependent exopeptidases	T: Zn-dependent exopeptidases	F: PBP_dimer	ECOD (develop294)

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	Beta-lactam-inducible penicillin-binding protein	glycosyltransferase activity transferase activity catalytic activity 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 carboxypeptidase activity organic acid binding glycosyltransferase activity transferase activity catalytic activity 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 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	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.