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3kx2

Crystal structure of Prp43p in complex with ADP

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

Pre-mRNA-splicing factor ATP-dependent RNA helicase PRP43

Saccharomyces cerevisiae

UniProt P53131

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 ADENOSINE-5'-DIPHOSPHATE × 1 water × 1 Consistent with protein count
2 Protein monomer Monomer Protein 1 MAGNESIUM ION × 1 ADENOSINE-5'-DIPHOSPHATE × 1 water × 1 Consistent with protein count

Other States of the Same Protein in the Database

Monomer
2xau 2xau 3kx2 3kx2 5jpt 5jpt

6 assemblies

Homodimer

None

Homotetramer

None

Other homooligomers

None

Heteromeric or nucleic-acid complex
5i8q 5i8q 5y88 8rdy

4 assemblies

View Construct and Data Evidence
UniProt name PRP43_YEAST
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–767； UniProt 1–767 Author chain B； PDBConstruct 1–767； UniProt 1–767

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_id3kx2
Deposition date deposition_date2009-12-02
Structure title titleCrystal structure of Prp43p in complex with ADP
Keywords keywordsRec-A domains, OB fold, winged-helix domain, ATP-binding, mRNA processing, mRNA splicing, Nucleotide-binding, HYDROLASE; HYDROLASE
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.

3kx2__assembly_1__model_1

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

Download this curve (.dat)

3kx2__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.

3kx2__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）28.99 Å
Rg (electron density)27.88 Å
Total Rg28.58 Å
Atom count6095
Residues755
Excluded volume108300 ų
Maximum q0.500 Å⁻¹
Assembly Model Structure unit Oligomeric description Status CRYSOL Actions
1 1 3kx2__assembly_1__model_1 monomeric （1） Success 4.1.3-1-20251215 (887e7ef) View Download
2 1 3kx2__assembly_2__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 (4)

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6. Fold Classification (SCOP + CATH) 16 domains

SCOP 2.08 (10 domains)

Domain ID domain_idd3kx2a1
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.37 — P-loop containing nucleoside triphosphate hydrolases
Superfamily Superfamily superfamilyc.37.1 — P-loop containing nucleoside triphosphate hydrolases
Family Family familyc.37.1.19 — Tandem AAA-ATPase domain
Domain ID domain_idd3kx2a2
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.37 — P-loop containing nucleoside triphosphate hydrolases
Superfamily Superfamily superfamilyc.37.1 — P-loop containing nucleoside triphosphate hydrolases
Family Family familyc.37.1.19 — Tandem AAA-ATPase domain
Domain ID domain_idd3kx2a3
Class classa — All alpha proteins
Fold Fold folda.4 — DNA/RNA-binding 3-helical bundle
Superfamily Superfamily superfamilya.4.5 — 'Winged helix' DNA-binding domain
Family Family familya.4.5.87 — Helicase RNA-binding domain
Domain ID domain_idd3kx2a4
Class classa — All alpha proteins
Fold Fold folda.289 — Sec63 N-terminal domain-like
Superfamily Superfamily superfamilya.289.1 — Sec63 N-terminal domain-like
Family Family familya.289.1.3 — Helicase 'ratchet' domain
Domain ID domain_idd3kx2a5
Class classb — All beta proteins
Fold Fold foldb.40 — OB-fold
Superfamily Superfamily superfamilyb.40.4 — Nucleic acid-binding proteins
Family Family familyb.40.4.17 — RNA Helicase C-terminal domain-like
Domain ID domain_idd3kx2b1
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.37 — P-loop containing nucleoside triphosphate hydrolases
Superfamily Superfamily superfamilyc.37.1 — P-loop containing nucleoside triphosphate hydrolases
Family Family familyc.37.1.19 — Tandem AAA-ATPase domain
Domain ID domain_idd3kx2b2
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.37 — P-loop containing nucleoside triphosphate hydrolases
Superfamily Superfamily superfamilyc.37.1 — P-loop containing nucleoside triphosphate hydrolases
Family Family familyc.37.1.19 — Tandem AAA-ATPase domain
Domain ID domain_idd3kx2b3
Class classa — All alpha proteins
Fold Fold folda.4 — DNA/RNA-binding 3-helical bundle
Superfamily Superfamily superfamilya.4.5 — 'Winged helix' DNA-binding domain
Family Family familya.4.5.87 — Helicase RNA-binding domain
Domain ID domain_idd3kx2b4
Class classa — All alpha proteins
Fold Fold folda.289 — Sec63 N-terminal domain-like
Superfamily Superfamily superfamilya.289.1 — Sec63 N-terminal domain-like
Family Family familya.289.1.3 — Helicase 'ratchet' domain
Domain ID domain_idd3kx2b5
Class classb — All beta proteins
Fold Fold foldb.40 — OB-fold
Superfamily Superfamily superfamilyb.40.4 — Nucleic acid-binding proteins
Family Family familyb.40.4.17 — RNA Helicase C-terminal domain-like

CATH v4.4 (6 domains)

Domain ID domain_id3kx2A02
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily300 — P-loop containing nucleotide triphosphate hydrolases
Domain ID domain_id3kx2A03
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily300 — P-loop containing nucleotide triphosphate hydrolases
Domain ID domain_id3kx2A04
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology10 — Arc Repressor Mutant, subunit A
Homologous superfamily homologous superfamily2130 — DEAH helicase family, winged-helix domain
Domain ID domain_id3kx2B02
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily300 — P-loop containing nucleotide triphosphate hydrolases
Domain ID domain_id3kx2B03
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily300 — P-loop containing nucleotide triphosphate hydrolases
Domain ID domain_id3kx2B04
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology10 — Arc Repressor Mutant, subunit A
Homologous superfamily homologous superfamily2130 — DEAH helicase family, winged-helix domain
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7. Citations (1)