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1x3n

Crystal structure of AMPPNP bound Propionate kinase (TdcD) from Salmonella typhimurium

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

Propionate kinase

Salmonella typhimurium

UniProt O06961

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein homooligomer Homooligomer Protein 2 1,2-ETHANEDIOL × 2 PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 2 water × 2 Consistent with protein count

Other States of the Same Protein in the Database

Monomer

None

Homodimer
1x3m 1x3n 2e1y 2e1z 2e20 4fwk 4fwl 4fwm 4fwn 4fwo 4fwp 4fwq

17 assemblies; showing the first 12

Homotetramer

None

Other homooligomers

None

Heteromeric or nucleic-acid complex

None

View Construct and Data Evidence
UniProt name TDCD_SALTY
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 15–415； UniProt 2–402

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_id1x3n
Deposition date deposition_date2005-05-10
Structure title titleCrystal structure of AMPPNP bound Propionate kinase (TdcD) from Salmonella typhimurium
Keywords keywordsPropionate Kinase, TdcD, AMPPNP, L-threonine metabolism, Propionate Metabolism, 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.

1x3n__assembly_1__model_1

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

Download this curve (.dat)

1x3n__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.

1x3n__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）28.94 Å
Rg (electron density)28.47 Å
Total Rg29.04 Å
Atom count5938
Residues788
Excluded volume104760 ų
Maximum q0.500 Å⁻¹
Assembly Model Structure unit Oligomeric description Status CRYSOL Actions
1 1 1x3n__assembly_1__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 (4)

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6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_idd1x3na1
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.55 — Ribonuclease H-like motif
Superfamily Superfamily superfamilyc.55.1 — Actin-like ATPase domain
Family Family familyc.55.1.2 — Acetokinase-like
Domain ID domain_idd1x3na2
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.55 — Ribonuclease H-like motif
Superfamily Superfamily superfamilyc.55.1 — Actin-like ATPase domain
Family Family familyc.55.1.2 — Acetokinase-like

CATH v4.4 (2 domains)

Domain ID domain_id1x3nA01
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology420 — Nucleotidyltransferase; domain 5
Homologous superfamily homologous superfamily40 — ATPase, nucleotide binding domain
Domain ID domain_id1x3nA02
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology420 — Nucleotidyltransferase; domain 5
Homologous superfamily homologous superfamily40 — ATPase, nucleotide binding domain
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7. Citations (1)