4GKH | pdb_00004gkh

Crystal structure of the aminoglycoside phosphotransferase APH(3')-Ia, with substrate kanamycin and small molecule inhibitor 1-NA-PP1

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)
A	d4gkha_	Alpha and beta proteins (a+b)	Protein kinase-like (PK-like)	Protein kinase-like (PK-like)	automated matches	automated matches	(Acinetobacter baumannii AYE ) [TaxId: 509173 ],	SCOPe (2.08)
B	d4gkhb_	Alpha and beta proteins (a+b)	Protein kinase-like (PK-like)	Protein kinase-like (PK-like)	automated matches	automated matches	(Acinetobacter baumannii AYE ) [TaxId: 509173 ],	SCOPe (2.08)
C	d4gkhc_	Alpha and beta proteins (a+b)	Protein kinase-like (PK-like)	Protein kinase-like (PK-like)	automated matches	automated matches	(Acinetobacter baumannii AYE ) [TaxId: 509173 ],	SCOPe (2.08)
D	d4gkhd_	Alpha and beta proteins (a+b)	Protein kinase-like (PK-like)	Protein kinase-like (PK-like)	automated matches	automated matches	(Acinetobacter baumannii AYE ) [TaxId: 509173 ],	SCOPe (2.08)
E	d4gkhe_	Alpha and beta proteins (a+b)	Protein kinase-like (PK-like)	Protein kinase-like (PK-like)	automated matches	automated matches	(Acinetobacter baumannii AYE ) [TaxId: 509173 ],	SCOPe (2.08)
F	d4gkhf_	Alpha and beta proteins (a+b)	Protein kinase-like (PK-like)	Protein kinase-like (PK-like)	automated matches	automated matches	(Acinetobacter baumannii AYE ) [TaxId: 509173 ],	SCOPe (2.08)
G	d4gkhg_	Alpha and beta proteins (a+b)	Protein kinase-like (PK-like)	Protein kinase-like (PK-like)	automated matches	automated matches	(Acinetobacter baumannii AYE ) [TaxId: 509173 ],	SCOPe (2.08)
H	d4gkhh_	Alpha and beta proteins (a+b)	Protein kinase-like (PK-like)	Protein kinase-like (PK-like)	automated matches	automated matches	(Acinetobacter baumannii AYE ) [TaxId: 509173 ],	SCOPe (2.08)
I	d4gkhi_	Alpha and beta proteins (a+b)	Protein kinase-like (PK-like)	Protein kinase-like (PK-like)	automated matches	automated matches	(Acinetobacter baumannii AYE ) [TaxId: 509173 ],	SCOPe (2.08)
J	d4gkhj_	Alpha and beta proteins (a+b)	Protein kinase-like (PK-like)	Protein kinase-like (PK-like)	automated matches	automated matches	(Acinetobacter baumannii AYE ) [TaxId: 509173 ],	SCOPe (2.08)
K	d4gkhk_	Alpha and beta proteins (a+b)	Protein kinase-like (PK-like)	Protein kinase-like (PK-like)	automated matches	automated matches	(Acinetobacter baumannii AYE ) [TaxId: 509173 ],	SCOPe (2.08)
L	d4gkhl_	Alpha and beta proteins (a+b)	Protein kinase-like (PK-like)	Protein kinase-like (PK-like)	automated matches	automated matches	(Acinetobacter baumannii AYE ) [TaxId: 509173 ],	SCOPe (2.08)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A		e4gkhA1	A: alpha arrays	X: Flavodoxin-like	H: Precorrin-8X methylmutase CbiC/CobH	T: Precorrin-8X methylmutase CbiC/CobH	F:	ECOD (v295.2)
B	14-3-3	e4gkhB1	A: alpha arrays	X: beta-Grasp	H: Ubiquitin-related	T: Ubiquitin-like	F: 14-3-3	ECOD (v295.2)
C	14-3-3	e4gkhC1	A: alpha arrays	X: beta-Grasp	H: Ubiquitin-related	T: Ubiquitin-like	F: 14-3-3	ECOD (v295.2)
D	14-3-3	e4gkhD1	A: alpha arrays	X: beta-Grasp	H: Ubiquitin-related	T: Ubiquitin-like	F: 14-3-3	ECOD (v295.2)
E	14-3-3	e4gkhE1	A: alpha arrays	X: beta-Grasp	H: Ubiquitin-related	T: Ubiquitin-like	F: 14-3-3	ECOD (v295.2)
F	14-3-3	e4gkhF1	A: alpha arrays	X: beta-Grasp	H: Ubiquitin-related	T: Ubiquitin-like	F: 14-3-3	ECOD (v295.2)
G	14-3-3	e4gkhG1	A: alpha arrays	X: beta-Grasp	H: Ubiquitin-related	T: Ubiquitin-like	F: 14-3-3	ECOD (v295.2)
H	14-3-3	e4gkhH1	A: alpha arrays	X: beta-Grasp	H: Ubiquitin-related	T: Ubiquitin-like	F: 14-3-3	ECOD (v295.2)
I	14-3-3	e4gkhI1	A: alpha arrays	X: beta-Grasp	H: Ubiquitin-related	T: Ubiquitin-like	F: 14-3-3	ECOD (v295.2)
J	14-3-3	e4gkhJ1	A: alpha arrays	X: beta-Grasp	H: Ubiquitin-related	T: Ubiquitin-like	F: 14-3-3	ECOD (v295.2)
K	14-3-3	e4gkhK1	A: alpha arrays	X: beta-Grasp	H: Ubiquitin-related	T: Ubiquitin-like	F: 14-3-3	ECOD (v295.2)
L	14-3-3	e4gkhL1	A: alpha arrays	X: beta-Grasp	H: Ubiquitin-related	T: Ubiquitin-like	F: 14-3-3	ECOD (v295.2)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.30.200.20	Alpha Beta	2-Layer Sandwich	Phosphorylase Kinase	domain 1	CATH (4.3.0)
A	3.90.1200.10	Alpha Beta	Alpha-Beta Complex	Aminoglycoside 3'-phosphotransferase	Chain: A, domain 2	CATH (4.3.0)
B	3.30.200.20	Alpha Beta	2-Layer Sandwich	Phosphorylase Kinase	domain 1	CATH (4.3.0)
B	3.90.1200.10	Alpha Beta	Alpha-Beta Complex	Aminoglycoside 3'-phosphotransferase	Chain: A, domain 2	CATH (4.3.0)
C	3.30.200.20	Alpha Beta	2-Layer Sandwich	Phosphorylase Kinase	domain 1	CATH (4.3.0)
C	3.90.1200.10	Alpha Beta	Alpha-Beta Complex	Aminoglycoside 3'-phosphotransferase	Chain: A, domain 2	CATH (4.3.0)
D	3.30.200.20	Alpha Beta	2-Layer Sandwich	Phosphorylase Kinase	domain 1	CATH (4.3.0)
D	3.90.1200.10	Alpha Beta	Alpha-Beta Complex	Aminoglycoside 3'-phosphotransferase	Chain: A, domain 2	CATH (4.3.0)
E	3.30.200.20	Alpha Beta	2-Layer Sandwich	Phosphorylase Kinase	domain 1	CATH (4.3.0)
E	3.90.1200.10	Alpha Beta	Alpha-Beta Complex	Aminoglycoside 3'-phosphotransferase	Chain: A, domain 2	CATH (4.3.0)
F	3.30.200.20	Alpha Beta	2-Layer Sandwich	Phosphorylase Kinase	domain 1	CATH (4.3.0)
F	3.90.1200.10	Alpha Beta	Alpha-Beta Complex	Aminoglycoside 3'-phosphotransferase	Chain: A, domain 2	CATH (4.3.0)
G	3.30.200.20	Alpha Beta	2-Layer Sandwich	Phosphorylase Kinase	domain 1	CATH (4.3.0)
G	3.90.1200.10	Alpha Beta	Alpha-Beta Complex	Aminoglycoside 3'-phosphotransferase	Chain: A, domain 2	CATH (4.3.0)
H	3.30.200.20	Alpha Beta	2-Layer Sandwich	Phosphorylase Kinase	domain 1	CATH (4.3.0)
H	3.90.1200.10	Alpha Beta	Alpha-Beta Complex	Aminoglycoside 3'-phosphotransferase	Chain: A, domain 2	CATH (4.3.0)
I	3.30.200.20	Alpha Beta	2-Layer Sandwich	Phosphorylase Kinase	domain 1	CATH (4.3.0)
I	3.90.1200.10	Alpha Beta	Alpha-Beta Complex	Aminoglycoside 3'-phosphotransferase	Chain: A, domain 2	CATH (4.3.0)
J	3.30.200.20	Alpha Beta	2-Layer Sandwich	Phosphorylase Kinase	domain 1	CATH (4.3.0)
J	3.90.1200.10	Alpha Beta	Alpha-Beta Complex	Aminoglycoside 3'-phosphotransferase	Chain: A, domain 2	CATH (4.3.0)
K	3.30.200.20	Alpha Beta	2-Layer Sandwich	Phosphorylase Kinase	domain 1	CATH (4.3.0)
K	3.90.1200.10	Alpha Beta	Alpha-Beta Complex	Aminoglycoside 3'-phosphotransferase	Chain: A, domain 2	CATH (4.3.0)
L	3.30.200.20	Alpha Beta	2-Layer Sandwich	Phosphorylase Kinase	domain 1	CATH (4.3.0)
L	3.90.1200.10	Alpha Beta	Alpha-Beta Complex	Aminoglycoside 3'-phosphotransferase	Chain: A, domain 2	CATH (4.3.0)

AMR Gene: CARD Annotation CARD Database Homepage

Chains	Accession	Short Name	Description	Provenance Source (Version)
A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L	ARO:3002641	APH(3')-Ia	APH(3')-Ia is a transposon-encoded aminoglycoside phosphotransferase in E. coli and S. enterica. It is identical at the protein sequence to APH(3')-Ic, an aminoglycoside phosphotransferase encoded by plasmids, transposons and genomic islands in K. pneumoniae, A. baumannii, S. marcescens, Corynebacterium spp., Photobacterium spp. and Citrobacter spp.	CARD (4.0.2)

AMR Gene Family: CARD Annotation CARD Database Homepage

Chains	Accession	Gene Family	Drug Class	Resistance Machanism	Provenance Source (Version)
A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L	ARO:3000126	APH(3')	aminoglycoside antibiotic	antibiotic inactivation	CARD (4.0.2)

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, I, J, K, L	Aminoglycoside 3'-phosphotransferase AphA1-IAB	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	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L	IPR051678	Aminoglycoside Phosphotransferase Enzymes	Family
A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L	IPR024165	Aminoglycoside 3-phosphotransferase	Family
A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L	IPR002575	Aminoglycoside phosphotransferase	Domain
A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L	IPR011009	Protein kinase-like domain superfamily	Homologous Superfamily

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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.