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2pb9

Crystal structure of C-terminal domain of phosphomethylpyrimidine kinase

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

Phosphomethylpyrimidine kinase

Pyrococcus furiosus

UniProt Q8U193

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein homooligomer Homooligomer Protein 4 PHOSPHATE ION × 4 water × 4 Consistent with protein count

Other States of the Same Protein in the Database

Monomer

None

Homodimer

None

Homotetramer
2pb9

1 assemblies

Other homooligomers

None

Heteromeric or nucleic-acid complex

None

View Construct and Data Evidence
UniProt name Q8U193_PYRFU
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 4–187； UniProt 268–451 Author chain B； PDBConstruct 4–187； UniProt 268–451

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_id2pb9
Deposition date deposition_date2007-03-28
Structure title titleCrystal structure of C-terminal domain of phosphomethylpyrimidine kinase
Keywords keywords;phosphate, psi2, 10417c, NYSGXRC, Structural Genomics, Protein Structure Initiative, New York SGX Research Center for Structural Genomics, 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.

2pb9__assembly_1__model_1

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

Download this curve (.dat)

2pb9__assembly_1__model_1 | I(q)

10-2 10-1 106 107 108 q (1/Angstrom) I(q)
100 plotted points; both axes use logarithmic scales.

2pb9__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）29.52 Å
Rg (electron density)28.82 Å
Total Rg29.50 Å
Atom count5904
Residues724
Excluded volume106050 ų
Maximum q0.500 Å⁻¹
Assembly Model Structure unit Oligomeric description Status CRYSOL Actions
1 1 2pb9__assembly_1__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 (3)

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6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_idd2pb9a1
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.74 — AraD/HMP-PK domain-like
Superfamily Superfamily superfamilyc.74.1 — AraD/HMP-PK domain-like
Family Family familyc.74.1.2 — Phosphomethylpyrimidine kinase C-terminal domain-like
Domain ID domain_idd2pb9b_
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.74 — AraD/HMP-PK domain-like
Superfamily Superfamily superfamilyc.74.1 — AraD/HMP-PK domain-like
Family Family familyc.74.1.2 — Phosphomethylpyrimidine kinase C-terminal domain-like

CATH v4.4 (2 domains)

Domain ID domain_id2pb9A00
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology225 — L-fuculose-1-phosphate Aldolase
Homologous superfamily homologous superfamily10 — Class II aldolase/adducin N-terminal domain
Domain ID domain_id2pb9B00
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology225 — L-fuculose-1-phosphate Aldolase
Homologous superfamily homologous superfamily10 — Class II aldolase/adducin N-terminal domain
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7. Citations (1)