SAXSdb — 5ya2

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

Autoinducer-2 kinase

Escherichia coli (strain K12)

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 2	Phosphocarrier protein HPr × 1 （P0AA04） ADENOSINE-5'-DIPHOSPHATE × 1 HEXANE-1,6-DIOL × 1 PHOSPHATE ION × 4 water × 2	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 2	Phosphocarrier protein HPr × 1 （P0AA04） ADENOSINE-5'-DIPHOSPHATE × 1 HEXANE-1,6-DIOL × 1 PHOSPHATE ION × 2 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	LSRK_ECOLI
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 11–540； UniProt 1–530 Author chain B； PDBConstruct 11–540； UniProt 1–530

Phosphocarrier protein HPr

Escherichia coli (strain K12)

UniProt P0AA04

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 2	Autoinducer-2 kinase × 1 （P77432） ADENOSINE-5'-DIPHOSPHATE × 1 HEXANE-1,6-DIOL × 1 PHOSPHATE ION × 4 water × 2	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 2	Autoinducer-2 kinase × 1 （P77432） ADENOSINE-5'-DIPHOSPHATE × 1 HEXANE-1,6-DIOL × 1 PHOSPHATE ION × 2 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	PTHP_ECOLI
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain C； PDBConstruct 1–85； UniProt 1–85 Author chain D； PDBConstruct 1–85； UniProt 1–85

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	5ya2
Deposition date deposition_date	2017-08-30
Structure title title	Crystal structure of LsrK-HPr complex with ADP
Keywords keywords	Quorum sensing, LsrK, HPr, complex, ADP binding, STRUCTURAL PROTEIN; STRUCTURAL PROTEIN
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.

5ya2__assembly_1__model_1

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

Download this curve (.dat)

5ya2__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

5ya2__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	26.95 Å
Rg (electron density)	26.28 Å
Total Rg	26.98 Å
Atom count	4318
Residues	563
Excluded volume	76583 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`5ya2__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`5ya2__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 (6)

Entity 1 Entity 1 polymer

Description description	Autoinducer-2 kinase
Molecular weight formula_weight	58854.8 kDa
EC 编号 ec_number	2.7.1.189
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	8686

HHHHHHSEDPMARLFTLSESKYYLMALDAGTGSIRAVIFDLEGNQIAVGQAEWRHLAVPDVPGSMEFDLNKNWQLACECMRQALHNAGIAPEYIAAVSACSMREGIVLYNNEGAPIWACANVDARAAREVSELKELHNNTFENEVYRATGQTLALSAIPRLLWLAHHRSDIYRQASTITMISDWLAYMLSGELAVDPSNAGTTGLLDLTTRDWKPALLDMAGLRADILSPVKETGTLLGVVSSQAAELCGLKAGTPVVVGGGDVQLGCLGLGVVRPAQTAVLGGTFWQQVVNLAAPVTDPEMNVRVNPHVIPGMVQAESISFFTGLTMRWFRDAFCAEEKLIAERLGIDTYTLLEEMASRVPPGSWGVMPIFSDRMRFKTWYHAAPSFINLSIDPDKCNKATLFRALEENAAIVSACNLQQIADFSNIHPSSLVFAGGGSKGKLWSQILADVSGLPVNIPVVKEATALGCAIAAGVGAGIFSSMAETGERLVRWERTHTPDPEKHELYQDSRDKWQAVYQDQLGLVDHGLTTSLWKAPGL

Source Source

Source organism organism	Escherichia coli (strain K12)
NCBI taxonomy ID ncbi_taxonomy_id	83333
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	Phosphocarrier protein HPr
Molecular weight formula_weight	9129.3 kDa
EC 编号 ec_number	2.7.11.-
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

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

MFQQEVTITAPNGLHTRPAAQFVKEAKGFTSEITVTSNGKSASAKSLFKLQTLGLTQGTVVTISAEGEDEQKAVEHLVKLMAELE

Source Source

Source organism organism	Escherichia coli (strain K12)
NCBI taxonomy ID ncbi_taxonomy_id	83333
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	HEXANE-1,6-DIOL
Molecular weight formula_weight	118.2 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 5 Entity 5 non-polymer

Description description	PHOSPHATE ION
Molecular weight formula_weight	95.0 kDa
Source method src_method	syn
Copy count entity_count	6

Entity 6 Entity 6 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	60

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6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d5ya2c_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.94 — HPr-like
Superfamily Superfamily superfamily	d.94.1 — HPr-like
Family Family family	d.94.1.1 — HPr-like

Domain ID domain_id	d5ya2d_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.94 — HPr-like
Superfamily Superfamily superfamily	d.94.1 — HPr-like
Family Family family	d.94.1.1 — HPr-like

CATH v4.4 (2 domains)

Domain ID domain_id	5ya2C00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1340 — Histidine-containing Protein; Chain: A;
Homologous superfamily homologous superfamily	10 — HPr-like

Domain ID domain_id	5ya2D00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1340 — Histidine-containing Protein; Chain: A;
Homologous superfamily homologous superfamily	10 — HPr-like

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Unit-cell length a length_a	101.251 Å
Unit-cell length b length_b	101.251 Å
Unit-cell length c length_c	344.149 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	12

Space group space_group	P 32 2 1
Space-group number int_tables_number	154
Crystal system crystal_system	—

Resolution resolution	2.701 Å
Low-resolution limit resolution_low	46.316 Å
R factor r_factor	0.2152
R_work r_work	0.2137
R_free r_free	0.2546

Crystal structure of LsrK-HPr complex with ADP

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

Autoinducer-2 kinase

State in the Current Structure

Other States of the Same Protein in the Database

Phosphocarrier protein HPr

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

5ya2__assembly_1__model_1

5ya2__assembly_1__model_1 | I(q)

5ya2__assembly_1__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 (6)

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 non-polymer

Entity 6 Entity 6 water

6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

7. Citations (1)

Crystal structure of LsrK-HPr complex with ADP

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

Autoinducer-2 kinase

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Phosphocarrier protein HPr

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

5ya2__assembly_1__model_1

5ya2__assembly_1__model_1 | I(q)

5ya2__assembly_1__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 (6)

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 non-polymer

Entity 6 Entity 6 water

6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

7. Citations (1)