6P08 | pdb_00006p08

Ternary structure of the E52D mutant of ANT-4'' with Neomycin, AMP and Pyrophosphate

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)
A	d6p08a2	All alpha proteins	Four-helical up-and-down bundle	Nucleotidyltransferase substrate binding subunit/domain	Kanamycin nucleotidyltransferase (KNTase), C-terminal domain	automated matches	(Bacillus sp. (in: firmicutes) ) [TaxId: 1409 ],	SCOPe (2.08)
A	d6p08a1	Alpha and beta proteins (a+b)	Nucleotidyltransferase	Nucleotidyltransferase	Kanamycin nucleotidyltransferase (KNTase), N-terminal domain	automated matches	(Bacillus sp. (in: firmicutes) ) [TaxId: 1409 ],	SCOPe (2.08)
B [auth D]	d6p08d2	All alpha proteins	Four-helical up-and-down bundle	Nucleotidyltransferase substrate binding subunit/domain	Kanamycin nucleotidyltransferase (KNTase), C-terminal domain	automated matches	(Bacillus sp. (in: firmicutes) ) [TaxId: 1409 ],	SCOPe (2.08)
B [auth D]	d6p08d1	Alpha and beta proteins (a+b)	Nucleotidyltransferase	Nucleotidyltransferase	Kanamycin nucleotidyltransferase (KNTase), N-terminal domain	automated matches	(Bacillus sp. (in: firmicutes) ) [TaxId: 1409 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	Nucleotidyltransferase-like	8042135	3000129	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	HEPN domain-like	8042134	3000904	SCOP2B (2022-06-29)
B [auth D]	SCOP2B Superfamily	Nucleotidyltransferase-like	8042135	3000129	SCOP2B (2022-06-29)
B [auth D]	SCOP2B Superfamily	HEPN domain-like	8042134	3000904	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)
A	KNTase_C	e6p08A2	A: alpha bundles	X: Four-helical up-and-down bundle	H: HEPN	T: Nucleotidyltransferase substrate binding subunit/domain	F: KNTase_C	ECOD (1.6)
A	NTP_transf_2	e6p08A1	A: a+b three layers	X: Nucleotidyltransferase-like	H: Nucleotidyltransferase (From Topology)	T: Nucleotidyltransferase	F: NTP_transf_2	ECOD (1.6)
B [auth D]	KNTase_C	e6p08D1	A: alpha bundles	X: Four-helical up-and-down bundle	H: HEPN	T: Nucleotidyltransferase substrate binding subunit/domain	F: KNTase_C	ECOD (1.6)
B [auth D]	NTP_transf_2	e6p08D2	A: a+b three layers	X: Nucleotidyltransferase-like	H: Nucleotidyltransferase (From Topology)	T: Nucleotidyltransferase	F: NTP_transf_2	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.30.460.10	Alpha Beta	2-Layer Sandwich	Beta Polymerase	domain 2	CATH (utative)
A	1.20.120.330	Mainly Alpha	Up-down Bundle	Four Helix Bundle (Hemerythrin (Met), subunit A)	Nucleotidyltransferases domain 2	CATH (utative)
B [auth D]	3.30.460.10	Alpha Beta	2-Layer Sandwich	Beta Polymerase	domain 2	CATH (utative)
B [auth D]	1.20.120.330	Mainly Alpha	Up-down Bundle	Four Helix Bundle (Hemerythrin (Met), subunit A)	Nucleotidyltransferases domain 2	CATH (utative)

AMR Gene: CARD Annotation CARD Database Homepage

Chains	Accession	Short Name	Description	Provenance Source (Version)
A, B [auth D]	ARO:3002623	ANT(4')-Ia	ANT(4')-Ia is a plasmid-encoded aminoglycoside nucleotidyltransferase in S. epidermidis, S. aureus, Enterococcus spp. and Bacillus 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, B [auth D]	ARO:3000229	ANT(4')	aminoglycoside antibiotic	antibiotic inactivation	CARD (4.0.1)

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B [auth D]	Kanamycin nucleotidyltransferase	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 transferase activity nucleotidyltransferase activity catalytic activity 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 [auth D]	IPR043519	Nucleotidyltransferase superfamily	Homologous Superfamily
A, B [auth D]	IPR012481	Kanamycin nucleotidyltransferase, C-terminal	Domain

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.