SAXSdb — 2ajp

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

Pyridoxal kinase

Homo sapiens

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein monomer	Monomer	Protein 1	MAGNESIUM ION × 1 UNKNOWN ATOM OR ION × 20 PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 1	Consistent with protein count
2	Protein monomer	Monomer	Protein 1	MAGNESIUM ION × 1 UNKNOWN ATOM OR ION × 20 PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 1	Consistent with protein count
3	Protein homooligomer	Homooligomer	Protein 2	MAGNESIUM ION × 2 UNKNOWN ATOM OR ION × 40 PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	PDXK_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 20–326； UniProt 6–312 Author chain B； PDBConstruct 20–326； UniProt 6–312

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	2ajp
Deposition date deposition_date	2005-08-02
Structure title title	Crystal structure of a human pyridoxal kinase
Keywords keywords	pyridoxal kinase, structural genomics, Structural Genomics Consortium, SGC, 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.

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2ajp__assembly_1__model_1`	monomeric （1）	Excluded	—	—
	Exclusion reason： The source record does not identify the atom or ion element unambiguously, so a reliable calculation is not possible.
2	1	`2ajp__assembly_2__model_1`	monomeric （1）	Excluded	—	—
	Exclusion reason： The source record does not identify the atom or ion element unambiguously, so a reliable calculation is not possible.
3	1	`2ajp__assembly_3__model_1`	dimeric （2）	Excluded	—	—
	Exclusion reason： The source record does not identify the atom or ion element unambiguously, so a reliable calculation is not possible.

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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	36554.8 kDa
EC 编号 ec_number	2.7.1.35
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	4693

MGSSHHHHHHSSGLVPRGSRVLSIQSHVIRGYVGNRAATFPLQVLGFEIDAVNSVQFSNHTGYAHWKGQVLNSDELQELYEGLRLNNMNKYDYVLTGYTRDKSFLAMVVDIVQELKQQNPRLVYVCDPVLGDKWDGEGSMYVPEDLLPVYKEKVVPLADIITPNQFEAELLSGRKIHSQEEALRVMDMLHSMGPDTVVITSSDLPSPQGSNYLIVLGSQRRRNPAGSVVMERIRMDIRKVDAVFVGTGDLFAAMLLAWTHKHPNNLKVACEKTVSTLHHVLQRTIQCAKAQAGEGVRPSPMQLELRMVQSKRDIEDPEIVVQATVL

Source Source

Source organism organism	Homo sapiens
Common name common_name	human
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Escherichia coli BL21(DE3)

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	UNKNOWN ATOM OR ION
Source method src_method	syn
Copy count entity_count	40

Entity 4 Entity 4 non-polymer

Description description	PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
Molecular weight formula_weight	506.2 kDa
Source method src_method	syn
Copy count entity_count	2

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6. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d2ajpa1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.72 — Ribokinase-like
Superfamily Superfamily superfamily	c.72.1 — Ribokinase-like
Family Family family	c.72.1.5 — PfkB-like kinase

Domain ID domain_id	d2ajpa2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d2ajpb1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.72 — Ribokinase-like
Superfamily Superfamily superfamily	c.72.1 — Ribokinase-like
Family Family family	c.72.1.5 — PfkB-like kinase

Domain ID domain_id	d2ajpb2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

CATH v4.4 (2 domains)

Domain ID domain_id	2ajpA00
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

Domain ID domain_id	2ajpB00
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	92.132 Å
Unit-cell length b length_b	114.971 Å
Unit-cell length c length_c	169.261 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	16

Space group space_group	I 2 2 2
Space-group number int_tables_number	23
Crystal system crystal_system	—

Resolution resolution	2.500 Å
Low-resolution limit resolution_low	46.078 Å
R factor r_factor	—
R_work r_work	0.2414
R_free r_free	0.2834

Crystal structure of a human pyridoxal kinase

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

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 non-polymer

6. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (4 domains)

CATH v4.4 (2 domains)

7. Citations (1)

Crystal structure of a human pyridoxal kinase

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

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 non-polymer

6. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (4 domains)

CATH v4.4 (2 domains)

7. Citations (1)