SAXSdb — 1yhj

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

Pyridoxal Kinase

OrganismNot specified

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein monomer	Monomer	Protein 1	(2R)-2-{[6-(BENZYLOXY)-9-ISOPROPYL-9H-PURIN-2-YL]AMINO}BUTAN-1-OL × 1 water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	PDXK_SHEEP
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–312； UniProt 1–312

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	1yhj
Deposition date deposition_date	2005-01-09
Structure title title	Crystal Structure of Pyridoxal Kinase in Complex with Roscovitine and Derivatives
Keywords keywords	Alpha-beta structure, complexed with O6-(R)-roscovitine, 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.

1yhj__assembly_1__model_1

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

Download this curve (.dat)

1yhj__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1yhj__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	20.23 Å
Rg (electron density)	18.95 Å
Total Rg	19.88 Å
Atom count	2425
Residues	307
Excluded volume	43211 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1yhj__assembly_1__model_1`	monomeric （1）	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 (3)

Entity 1 Entity 1 polymer

Description description	Pyridoxal Kinase
Molecular weight formula_weight	34860.9 kDa
EC 编号 ec_number	2.7.1.35
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	2622

MEEECRVLSIQSHVVRGYVGNRAATFPLQVLGFEVDAVNSVQFSNHTGYSHWKGQVLNSDELQELYDGLKLNHVNQYDYVLTGYTRDKSFLAMVVDIVQELKQQNPRLVYVCDPVMGDQRNGEGAMYVPDDLLPVYREKVVPVADIITPNQFEAELLTGRKIHSQEEALEVMDMLHSMGPDTVVITSSNLLSPRGSDYLMALGSQRTRAPDGSVVTQRIRMEMHKVDAVFVGTGDLFAAMLLAWTHKHPNNLKVACEKTVSAMHHVLQRTIKCAKAKSGEGVKPSPAQLELRMVQSKKDIESPEIVVQATVL

Entity 2 Entity 2 non-polymer

Description description	(2R)-2-{[6-(BENZYLOXY)-9-ISOPROPYL-9H-PURIN-2-YL]AMINO}BUTAN-1-OL
Molecular weight formula_weight	355.4 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	197

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6. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d1yhja_
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

CATH v4.4 (1 domains)

Domain ID domain_id	1yhjA00
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	103.173 Å
Unit-cell length b length_b	103.173 Å
Unit-cell length c length_c	58.538 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	6

Space group space_group	P 31 2 1
Space-group number int_tables_number	152
Crystal system crystal_system	—

Resolution resolution	2.800 Å
Low-resolution limit resolution_low	20.000 Å
R factor r_factor	—
R_work r_work	0.2260
R_free r_free	0.2850

Crystal Structure of Pyridoxal Kinase in Complex with Roscovitine and Derivatives

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

1yhj__assembly_1__model_1

1yhj__assembly_1__model_1 | I(q)

1yhj__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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

CATH v4.4 (1 domains)

7. Citations (1)

Crystal Structure of Pyridoxal Kinase in Complex with Roscovitine and Derivatives

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

1yhj__assembly_1__model_1

1yhj__assembly_1__model_1 | I(q)

1yhj__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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

CATH v4.4 (1 domains)

7. Citations (1)