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1rfu

Crystal structure of pyridoxal kinase complexed with ADP and PLP

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

pyridoxal kinase

OrganismNot specified

UniProt P82197

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein homooligomer Homooligomer Protein 2 ZINC ION × 2 PYRIDOXAL-5'-PHOSPHATE × 2 ADENOSINE-5'-DIPHOSPHATE × 2 water × 2 Consistent with protein count
2 Protein homooligomer Homooligomer Protein 2 ZINC ION × 2 PYRIDOXAL-5'-PHOSPHATE × 2 ADENOSINE-5'-DIPHOSPHATE × 2 water × 2 Consistent with protein count
3 Protein homooligomer Homooligomer Protein 2 ZINC ION × 2 PYRIDOXAL-5'-PHOSPHATE × 2 ADENOSINE-5'-DIPHOSPHATE × 2 water × 2 Consistent with protein count
4 Protein homooligomer Homooligomer Protein 2 ZINC ION × 2 PYRIDOXAL-5'-PHOSPHATE × 2 ADENOSINE-5'-DIPHOSPHATE × 2 water × 2 Consistent with protein count

Other States of the Same Protein in the Database

Monomer
1ygj 1ygk 1yhj

3 assemblies

Homodimer
1lhp 1lhr 1rft 1rfu 1rfu 1rfu 1rfu 1rfv

8 assemblies

Homotetramer

None

Other homooligomers

None

Heteromeric or nucleic-acid complex

None

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 Author chain B； PDBConstruct 1–312； UniProt 1–312 Author chain C； PDBConstruct 1–312； UniProt 1–312 Author chain D； PDBConstruct 1–312； UniProt 1–312 Author chain E； PDBConstruct 1–312； UniProt 1–312 Author chain F； PDBConstruct 1–312； UniProt 1–312 Author chain G； PDBConstruct 1–312； UniProt 1–312 Author chain H； 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_id1rfu
Deposition date deposition_date2003-11-10
Structure title titleCrystal structure of pyridoxal kinase complexed with ADP and PLP
Keywords keywordsTRANSFERASE; 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.

1rfu__assembly_2__model_1

Assembly 2 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

1rfu__assembly_2__model_1 | I(q)

10-2 10-1 105 106 107 q (1/Angstrom) I(q)
100 plotted points; both axes use logarithmic scales.

1rfu__assembly_2__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）26.06 Å
Rg (electron density)25.06 Å
Total Rg25.90 Å
Atom count4964
Residues624
Excluded volume88096 ų
Maximum q0.500 Å⁻¹
Assembly Model Structure unit Oligomeric description Status CRYSOL Actions
1 1 1rfu__assembly_1__model_1 dimeric （2） Success 4.1.3-1-20251215 (887e7ef) View Download
2 1 1rfu__assembly_2__model_1 dimeric （2） Success 4.1.3-1-20251215 (887e7ef) View Download
3 1 1rfu__assembly_3__model_1 dimeric （2） Success 4.1.3-1-20251215 (887e7ef) View Download
4 1 1rfu__assembly_4__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 (5)

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6. Fold Classification (SCOP + CATH) 16 domains

SCOP 2.08 (8 domains)

Domain ID domain_idd1rfua_
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_idd1rfub_
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_idd1rfuc_
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_idd1rfud_
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_idd1rfue_
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_idd1rfuf_
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_idd1rfug_
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_idd1rfuh_
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 (8 domains)

Domain ID domain_id1rfuA00
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_id1rfuB00
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_id1rfuC00
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_id1rfuD00
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_id1rfuE00
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_id1rfuF00
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_id1rfuG00
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_id1rfuH00
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 (3)