SAXSdb — 3ibq

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

Pyridoxal kinase

Lactobacillus plantarum

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein monomer	Monomer	Protein 1	ADENOSINE-5'-TRIPHOSPHATE × 1 MAGNESIUM ION × 1 water × 1	Consistent with protein count
2	Protein homooligomer	Homooligomer	Protein 2	ADENOSINE-5'-TRIPHOSPHATE × 2 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	Q88YB5_LACPL
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 4–274； UniProt 2–272

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	3ibq
Deposition date deposition_date	2009-07-16
Structure title title	Crystal structure of pyridoxal kinase from Lactobacillus plantarum in complex with ATP
Keywords keywords	;Pyridoxal kinase, ATP, PSI-II, 11208c, Structural Genomics, Protein Structure Initiative, New York SGX Research Center for Structural Genomics, NYSGXRC, Kinase, Transferase ;; 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.

3ibq__assembly_1__model_1

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

Download this curve (.dat)

3ibq__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3ibq__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	18.89 Å
Rg (electron density)	17.67 Å
Total Rg	18.47 Å
Atom count	2069
Residues	268
Excluded volume	36807 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3ibq__assembly_1__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`3ibq__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 (4)

Entity 1 Entity 1 polymer

Description description	Pyridoxal kinase
Molecular weight formula_weight	30412.6 kDa
EC 编号 ec_number	2.7.1.35
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	2238

MSLSTMLVAEDLSAVGGISLSSALPVLTAMQYDVAALPTSLLSTHTSGYGTPAVVDLSTWLPQVFAHWTRAQLHFDQALIGYVGSVALCQQITTYLEQQTLSLLVVDPVLGDLGQLYQGFDQDYVAAMRQLIQQADVILPNTTEAALLTGAPYQVTPDLEVILPALQAQLKTGAHAVITDVQRADQIGCAWLDEAGHVQYCGARRLPGHYNGTGDTLAAVIAGLLGRGYPLAPTLARANQWLNMAVAETIAQNRTDDRQGVALGDLLQAILALNEGHHHHHH

Source Source

Source organism organism	Lactobacillus plantarum
NCBI taxonomy ID ncbi_taxonomy_id	1590
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	ADENOSINE-5'-TRIPHOSPHATE
Molecular weight formula_weight	507.2 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 3 Entity 3 non-polymer

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	169

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6. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

Domain ID domain_id	3ibqA00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	1190 — UDP-N-acetylmuramoyl-L-alanine:D-glutamate ligase
Homologous superfamily homologous superfamily	20 — Ribokinase

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Unit-cell length a length_a	64.357 Å
Unit-cell length b length_b	69.576 Å
Unit-cell length c length_c	132.369 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	C 2 2 21
Space-group number int_tables_number	20
Crystal system crystal_system	—

Resolution resolution	2.000 Å
Low-resolution limit resolution_low	38.460 Å
R factor r_factor	0.1776
R_work r_work	0.1753
R_free r_free	0.2195

Crystal structure of pyridoxal kinase from Lactobacillus plantarum in complex with ATP

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

Pyridoxal kinase

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

3ibq__assembly_1__model_1

3ibq__assembly_1__model_1 | I(q)

3ibq__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 (4)

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 water

6. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

7. Citations (1)

Crystal structure of pyridoxal kinase from Lactobacillus plantarum in complex with ATP

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

Pyridoxal 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

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

3ibq__assembly_1__model_1

3ibq__assembly_1__model_1 | I(q)

3ibq__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 (4)

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 water

6. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

7. Citations (1)