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2yxt

Human Pyridoxal Kinase

Method: X-RAY DIFFRACTION
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Pyridoxal kinase

Homo sapiens

UniProt O00764

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein homooligomer Homooligomer Protein 2 SODIUM ION × 2 PHOSPHATE ION × 6 (4S)-2-METHYL-2,4-PENTANEDIOL × 14 water × 2 Consistent with protein count
2 Protein homooligomer Homooligomer Protein 4 SODIUM ION × 4 PHOSPHATE ION × 12 (4S)-2-METHYL-2,4-PENTANEDIOL × 28 water × 4 Consistent with protein count

Other States of the Same Protein in the Database

Monomer
2ajp 2ajp

2 assemblies

Homodimer
2ajp 2f7k 2yxt 2yxu 3fhx 3fhy 3keu 4en4 4eoh

9 assemblies

Homotetramer
2yxt 2yxu

2 assemblies

Other homooligomers

None

Heteromeric or nucleic-acid complex
8wr2

1 assemblies

View Construct and Data Evidence
UniProt name PDXK_HUMAN
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–312； UniProt 1–312 Author chain B； 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_id2yxt
Deposition date deposition_date2007-04-27
Structure title titleHuman Pyridoxal Kinase
Keywords keywordsbeta sheet with alpha helix, metal ion, TRANSFERASE; TRANSFERASE
Experimental Method methodX-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.

2yxt__assembly_1__model_1

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

Download this curve (.dat)

2yxt__assembly_1__model_1 | I(q)

10-2 10-1 106 107 q (1/Angstrom) I(q)
100 plotted points; both axes use logarithmic scales.

2yxt__assembly_1__model_1 | P(r) · Pending

The new assembly/model P(r) has not been calculated yet This placeholder does not display legacy data r (Angstrom) P(r)
P(r) will be calculated and displayed separately for the same assembly/model.
Rg（Guinier）26.60 Å
Rg (electron density)25.53 Å
Total Rg26.46 Å
Atom count4941
Residues608
Excluded volume88578 ų
Maximum q0.500 Å⁻¹
Assembly Model Structure unit Oligomeric description Status CRYSOL Actions
1 1 2yxt__assembly_1__model_1 dimeric （2） Success 4.1.3-1-20251215 (887e7ef) View Download
2 1 2yxt__assembly_2__model_1 tetrameric （4） 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)

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6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_idd2yxta_
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.72 — Ribokinase-like
Superfamily Superfamily superfamilyc.72.1 — Ribokinase-like
Family Family familyc.72.1.5 — PfkB-like kinase
Domain ID domain_idd2yxtb_
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.72 — Ribokinase-like
Superfamily Superfamily superfamilyc.72.1 — Ribokinase-like
Family Family familyc.72.1.5 — PfkB-like kinase

CATH v4.4 (2 domains)

Domain ID domain_id2yxtA00
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology1190 — UDP-N-acetylmuramoyl-L-alanine:D-glutamate ligase
Homologous superfamily homologous superfamily20 — Ribokinase
Domain ID domain_id2yxtB00
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology1190 — UDP-N-acetylmuramoyl-L-alanine:D-glutamate ligase
Homologous superfamily homologous superfamily20 — Ribokinase
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7. Citations (1)