SAXSdb — 1kny

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1. Protein Identity and Related Structures Protein Identity & Related Structures

KANAMYCIN NUCLEOTIDYLTRANSFERASE

Staphylococcus aureus

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 2	MAGNESIUM ION × 2 DIPHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER × 2 KANAMYCIN A × 2 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	KANU_STAAU
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–253； UniProt 1–253 Author chain B； PDBConstruct 1–253； UniProt 1–253

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	1kny
Deposition date deposition_date	1995-07-07
Structure title title	KANAMYCIN NUCLEOTIDYLTRANSFERASE
Keywords keywords	ANTIBIOTIC RESISTANCE, TRANSFERASE, PLASMID; TRANSFERASE
Experimental Method method	X-RAY DIFFRACTION

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3. Official assembly/model SAXS Official SAXS Profiles

This page reads only the latest assembly calculations. Every curve maps to an explicit PDB entry, official biological assembly and coordinate model.

1kny__assembly_1__model_1

Assembly 1 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

1kny__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1kny__assembly_1__model_1 | P(r) · Pending

P(r) will be calculated and displayed separately for the same assembly/model.

Rg（Guinier）	24.14 Å
Rg (electron density)	23.16 Å
Total Rg	23.94 Å
Atom count	4188
Residues	506
Excluded volume	74151 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1kny__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download

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4. Crystallography and Experiment 4. Crystallography & Experiment

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5. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Description description	KANAMYCIN NUCLEOTIDYLTRANSFERASE
Molecular weight formula_weight	28873.6 kDa
EC 编号 ec_number	2.7.7.-
Mutation mutation	D80Y
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	4231

MNGPIIMTREERMKIVHEIKERILDKYGDDVKAIGVYGSLGRQTDGPYSDIEMMCVMSTEEAEFSHEWTTGEWKVEVNFYSEEILLDYASQVESDWPLTHGQFFSILPIYDSGGYLEKVYQTAKSVEAQTFHDAICALIVEELFEYAGKWRNIRVQGPTTFLPSLTVQVAMAGAMLIGLHHRICYTTSASVLTEAVKQSDLPSGYDHLCQFVMSGQLSDSEKLLESLENFWNGIQEWTERHGYIVDVSKRIPF

Source Source

Source organism organism	Staphylococcus aureus
NCBI taxonomy ID ncbi_taxonomy_id	1280
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 3 Entity 3 non-polymer

Description description	DIPHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER
Molecular weight formula_weight	505.2 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 4 Entity 4 non-polymer

Description description	KANAMYCIN A
Molecular weight formula_weight	484.5 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	43

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6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d1knya1
Class class	a — All alpha proteins
Fold Fold fold	a.24 — Four-helical up-and-down bundle
Superfamily Superfamily superfamily	a.24.16 — Nucleotidyltransferase substrate binding subunit/domain
Family Family family	a.24.16.1 — Kanamycin nucleotidyltransferase (KNTase), C-terminal domain

Domain ID domain_id	d1knya2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.218 — Nucleotidyltransferase
Superfamily Superfamily superfamily	d.218.1 — Nucleotidyltransferase
Family Family family	d.218.1.1 — Kanamycin nucleotidyltransferase (KNTase), N-terminal domain

Domain ID domain_id	d1knyb1
Class class	a — All alpha proteins
Fold Fold fold	a.24 — Four-helical up-and-down bundle
Superfamily Superfamily superfamily	a.24.16 — Nucleotidyltransferase substrate binding subunit/domain
Family Family family	a.24.16.1 — Kanamycin nucleotidyltransferase (KNTase), C-terminal domain

Domain ID domain_id	d1knyb2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.218 — Nucleotidyltransferase
Superfamily Superfamily superfamily	d.218.1 — Nucleotidyltransferase
Family Family family	d.218.1.1 — Kanamycin nucleotidyltransferase (KNTase), N-terminal domain

CATH v4.4 (4 domains)

Domain ID domain_id	1knyA01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	460 — Beta Polymerase; domain 2
Homologous superfamily homologous superfamily	10 — Beta Polymerase, domain 2

Domain ID domain_id	1knyA02
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	120 — Four Helix Bundle (Hemerythrin (Met), subunit A)
Homologous superfamily homologous superfamily	330 — Nucleotidyltransferases domain 2

Domain ID domain_id	1knyB01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	460 — Beta Polymerase; domain 2
Homologous superfamily homologous superfamily	10 — Beta Polymerase, domain 2

Domain ID domain_id	1knyB02
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	120 — Four Helix Bundle (Hemerythrin (Met), subunit A)
Homologous superfamily homologous superfamily	330 — Nucleotidyltransferases domain 2

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Unit-cell length a length_a	57.300 Å
Unit-cell length b length_b	102.200 Å
Unit-cell length c length_c	108.800 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	2.500 Å
Low-resolution limit resolution_low	30.000 Å
R factor r_factor	—
R_work r_work	0.1680
R_free r_free	—

KANAMYCIN NUCLEOTIDYLTRANSFERASE

1. Protein Identity and Related Structures Protein Identity & Related Structures

KANAMYCIN NUCLEOTIDYLTRANSFERASE

State in the Current Structure

Other States of the Same Protein in the Database

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

1kny__assembly_1__model_1

1kny__assembly_1__model_1 | I(q)

1kny__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

5. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

CATH v4.4 (4 domains)

7. Citations (1)

KANAMYCIN NUCLEOTIDYLTRANSFERASE

1. Protein Identity and Related Structures Protein Identity & Related Structures

KANAMYCIN NUCLEOTIDYLTRANSFERASE

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

1kny__assembly_1__model_1

1kny__assembly_1__model_1 | I(q)

1kny__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

5. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

CATH v4.4 (4 domains)

7. Citations (1)