2BKK | pdb_00002bkk

Crystal structure of Aminoglycoside Phosphotransferase APH(3')-IIIa in complex with the inhibitor AR_3a

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
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	d2bkkc_	Alpha and beta proteins (a+b)	Protein kinase-like (PK-like)	Protein kinase-like (PK-like)	APH phosphotransferases	Type IIIa 3',5'-aminoglycoside phosphotransferase	(Enterococcus faecalis ) [TaxId: 1351 ],	SCOPe (2.08)
A	d2bkka_	Alpha and beta proteins (a+b)	Protein kinase-like (PK-like)	Protein kinase-like (PK-like)	APH phosphotransferases	Type IIIa 3',5'-aminoglycoside phosphotransferase	(Enterococcus faecalis ) [TaxId: 1351 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
C	SCOP2B Superfamily	Protein kinase-like (PK-like)	8034205	3000066	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Protein kinase-like (PK-like)	8034205	3000066	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)
C	Fructosamin_kin	e2bkkC1	A: a+b complex topology	X: Protein kinase/SAICAR synthase/ATP-grasp (From Homology)	H: Protein kinase/SAICAR synthase/ATP-grasp	T: Protein kinase	F: Fructosamin_kin	ECOD (1.6)
A	Fructosamin_kin	e2bkkA1	A: a+b complex topology	X: Protein kinase/SAICAR synthase/ATP-grasp (From Homology)	H: Protein kinase/SAICAR synthase/ATP-grasp	T: Protein kinase	F: Fructosamin_kin	ECOD (1.6)
D	Ank_2	e2bkkD1	A: alpha superhelices	X: Repetitive alpha hairpins	H: Ankyrin repeat (From Topology)	T: Ankyrin repeat	F: Ank_2	ECOD (1.6)
B	Ank_2	e2bkkB1	A: alpha superhelices	X: Repetitive alpha hairpins	H: Ankyrin repeat (From Topology)	T: Ankyrin repeat	F: Ank_2	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
C	3.30.200.20	Alpha Beta	2-Layer Sandwich	Phosphorylase Kinase	domain 1	CATH (4.2.0)
C	3.90.1200.10	Alpha Beta	Alpha-Beta Complex	Aminoglycoside 3'-phosphotransferase	Chain: A, domain 2	CATH (4.2.0)
A	3.30.200.20	Alpha Beta	2-Layer Sandwich	Phosphorylase Kinase	domain 1	CATH (4.2.0)
A	3.90.1200.10	Alpha Beta	Alpha-Beta Complex	Aminoglycoside 3'-phosphotransferase	Chain: A, domain 2	CATH (4.2.0)
D	1.25.40.20	Mainly Alpha	Alpha Horseshoe	Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat	Ankyrin repeat-containing domain	CATH (4.2.0)
B	1.25.40.20	Mainly Alpha	Alpha Horseshoe	Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat	Ankyrin repeat-containing domain	CATH (4.2.0)

AMR Gene: CARD Annotation CARD Database Homepage

Chains	Accession	Short Name	Description	Provenance Source (Version)
A, C	ARO:3002647	APH(3')-IIIa	APH(3')-IIIa is a plasmid-encoded aminoglycoside phosphotransferase in S. aureus and Enterococcus spp.	CARD (4.0.1)

AMR Gene Family: CARD Annotation CARD Database Homepage

Chains	Accession	Gene Family	Drug Class	Resistance Machanism	Provenance Source (Version)
A, C	ARO:3000126	APH(3')	aminoglycoside antibiotic	antibiotic inactivation	CARD (4.0.1)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, C	PF01636	Phosphotransferase enzyme family (APH)	Phosphotransferase enzyme family	This family consists of bacterial antibiotic resistance proteins, which confer resistance to various aminoglycosides they include: aminoglycoside 3'-phosphotransferase or kanamycin kinase / neomycin-kanamycin phosphotransferase and streptomycin 3''-k ...	This family consists of bacterial antibiotic resistance proteins, which confer resistance to various aminoglycosides they include: aminoglycoside 3'-phosphotransferase or kanamycin kinase / neomycin-kanamycin phosphotransferase and streptomycin 3''-kinase or streptomycin 3''-phosphotransferase. The aminoglycoside phosphotransferases inactivate aminoglycoside antibiotics via phosphorylation [2]. This family also includes homoserine kinase. This family is related to fructosamine kinase Pfam:PF03881.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, C	AMINOGLYCOSIDE 3'-PHOSPHOTRANSFERASE	binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding small molecule binding kinase activity kanamycin kinase activity aminoglycoside phosphotransferase activity transferase activity catalytic activity phosphotransferase activity, alcohol group as acceptor transferase activity, transferring phosphorus-containing groups	response to stimulus response to chemical response to antibiotic	-
B, D	DESIGNED ANKYRIN REPEAT INHIBITOR AR_3A	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, C	IPR051678	Aminoglycoside Phosphotransferase Enzymes	Family
A, C	IPR024165	Aminoglycoside 3-phosphotransferase	Family
A, C	IPR002575	Aminoglycoside phosphotransferase	Domain
A, C	IPR011009	Protein kinase-like domain superfamily	Homologous Superfamily

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.