SAXSdb — 2bkk

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

;AMINOGLYCOSIDE 3'-PHOSPHOTRANSFERASE ;

ENTEROCOCCUS FAECALIS

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 2	DESIGNED ANKYRIN REPEAT INHIBITOR AR_3A × 1 ADENOSINE-5'-DIPHOSPHATE × 1 MAGNESIUM ION × 2 water × 2	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 2	DESIGNED ANKYRIN REPEAT INHIBITOR AR_3A × 1 ADENOSINE-5'-DIPHOSPHATE × 1 MAGNESIUM ION × 2 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	KKA3_ENTFA
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–264； UniProt 1–264 Author chain C； PDBConstruct 1–264； UniProt 1–264

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	2bkk
Deposition date deposition_date	2005-02-16
Structure title title	Crystal structure of Aminoglycoside Phosphotransferase APH(3')-IIIa in complex with the inhibitor AR_3a
Keywords keywords	;TRANSFERASE/PEPTIDE, TRANSFERASE-DESIGNED PROTEIN COMPLEX, ANKYRIN REPEAT, CO-CRYSTALLIZATION, INHIBITOR DESIGN, DRUG DESIGN, ENZYME INHIBITION, KINASE INHIBITION, DESIGNED REPEAT PROTEIN, ANTIBIOTIC RESISTANCE, ATP-BINDING, KINASE, PLASMID, TRANSFERASE, TRANSFERASE-PEPTIDE complex ;; TRANSFERASE/PEPTIDE
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.

2bkk__assembly_2__model_1

Assembly 2 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

2bkk__assembly_2__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2bkk__assembly_2__model_1 | P(r) · Pending

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

Rg（Guinier）	25.94 Å
Rg (electron density)	25.43 Å
Total Rg	26.20 Å
Atom count	3392
Residues	419
Excluded volume	60106 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2bkk__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`2bkk__assembly_2__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	;AMINOGLYCOSIDE 3'-PHOSPHOTRANSFERASE ;
Molecular weight formula_weight	30979.9 kDa
EC 编号 ec_number	2.7.1.95
Mutation mutation	YES
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,C
Atom count atom_count	7000

MAKMRISPELKKLIEKYRSVKDTEGMSPAKVYKLVGENENLYLKMTDSRYKGTTYDVEREKDMMLWLEGKLPVPKVLHFERHDGWSNLLMSEADGVLCSEEYEDEQSPEKIIELYAECIRLFHSIDISDCPYTNSLDSRLAELDYLLNNDLADVDSENWEEDTPFKDPRELYDFLKTEKPEEELVFSHGDLGDSNIFVKDGKVSGFIDLGRSGRADKWYDIAFCVRSIREDIGEEQYVELFFDLLGIKPDWEKIKYYILLDELF

Source Source

Source organism organism	ENTEROCOCCUS FAECALIS
NCBI taxonomy ID ncbi_taxonomy_id	1351
Host organism host_organism	ESCHERICHIA COLI

Entity 2 Entity 2 polymer

Description description	DESIGNED ANKYRIN REPEAT INHIBITOR AR_3A
Molecular weight formula_weight	18602.8 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B,D

MRGSHHHHHHGSDLGKKLLEAARAGQDDEVRILMANGADVNANDWFGITPLHLVVNNGHLEIIEVLLKYAADVNASDKSGWTPLHLAAYRGHLEIVEVLLKYGADVNAMDYQGYTPLHLAAEDGHLEIVEVLLKYGADVNAQDKFGKTAFDISIDNGNEDLAEILQKLN

Source Source

Source organism organism	SYNTHETIC CONSTRUCT
NCBI taxonomy ID ncbi_taxonomy_id	32630
Host organism host_organism	ESCHERICHIA COLI

Entity 3 Entity 3 non-polymer

Description description	ADENOSINE-5'-DIPHOSPHATE
Molecular weight formula_weight	427.2 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 4 Entity 4 non-polymer

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	347

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6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d2bkka_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.144 — Protein kinase-like (PK-like)
Superfamily Superfamily superfamily	d.144.1 — Protein kinase-like (PK-like)
Family Family family	d.144.1.6 — APH phosphotransferases

Domain ID domain_id	d2bkkc_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.144 — Protein kinase-like (PK-like)
Superfamily Superfamily superfamily	d.144.1 — Protein kinase-like (PK-like)
Family Family family	d.144.1.6 — APH phosphotransferases

CATH v4.4 (6 domains)

Domain ID domain_id	2bkkA01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	200 — Phosphorylase Kinase; domain 1
Homologous superfamily homologous superfamily	20 — Phosphorylase Kinase; domain 1

Domain ID domain_id	2bkkA02
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	1200 — Aminoglycoside 3'-phosphotransferase; Chain: A, domain 2
Homologous superfamily homologous superfamily	10 — Aminoglycoside phosphotransferase (APH), C-terminal lobe

Domain ID domain_id	2bkkB00
Class class	1 — Mainly Alpha
Architecture architecture	25 — Alpha Horseshoe
Topology topology	40 — Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat
Homologous superfamily homologous superfamily	20 — Ankyrin repeat-containing domain

Domain ID domain_id	2bkkC01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	200 — Phosphorylase Kinase; domain 1
Homologous superfamily homologous superfamily	20 — Phosphorylase Kinase; domain 1

Domain ID domain_id	2bkkC02
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	1200 — Aminoglycoside 3'-phosphotransferase; Chain: A, domain 2
Homologous superfamily homologous superfamily	10 — Aminoglycoside phosphotransferase (APH), C-terminal lobe

Domain ID domain_id	2bkkD00
Class class	1 — Mainly Alpha
Architecture architecture	25 — Alpha Horseshoe
Topology topology	40 — Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat
Homologous superfamily homologous superfamily	20 — Ankyrin repeat-containing domain

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Unit-cell length a length_a	59.670 Å
Unit-cell length b length_b	98.082 Å
Unit-cell length c length_c	81.300 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	110.01 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	2.150 Å
Low-resolution limit resolution_low	20.000 Å
R factor r_factor	0.2000
R_work r_work	0.1990
R_free r_free	0.2600

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

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

;AMINOGLYCOSIDE 3'-PHOSPHOTRANSFERASE ;

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

2bkk__assembly_2__model_1

2bkk__assembly_2__model_1 | I(q)

2bkk__assembly_2__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

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 (2 domains)

CATH v4.4 (6 domains)

7. Citations (1)

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

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

;AMINOGLYCOSIDE 3'-PHOSPHOTRANSFERASE ;

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

2bkk__assembly_2__model_1

2bkk__assembly_2__model_1 | I(q)

2bkk__assembly_2__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

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 (2 domains)

CATH v4.4 (6 domains)

7. Citations (1)