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13iu

E. coli DnaK bound to peptide PA9

Method: X-RAY DIFFRACTION Dmax: 76.9 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Chaperone protein DnaK

Escherichia coli

UniProt P0A6Z0

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count Chain A； UniProt 389–607 Not recorded A1DF0 peptide PA9 × 1 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；291.15 K；0.2 M NH4F and 2.2 M (NH4)2SO4 Resolution 1.87 Å R-free 0.263

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB Difference from Current Entry 13IU Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
13IQ E. coli DnaK bound to Telaprevir Deposited 2026-05-07 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 389–600（212 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 1.87 Å R-free 0.268
13IV E. coli DaK bound to peptide PA1, structure A Deposited 2026-05-08 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 389–607（219 aa）
Not recorded A1DFX peptide PA1-A × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291.15 K；0.2 M Na2SO4 and 2.2 M (NH4)2SO4
Resolution 3.23 Å R-free 0.296
13IV E. coli DaK bound to peptide PA1, structure A Deposited 2026-05-08 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 389–607（219 aa）
Not recorded A1DFX peptide PA1-A × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291.15 K；0.2 M Na2SO4 and 2.2 M (NH4)2SO4
Resolution 3.23 Å R-free 0.296
13JG E. coli DnaK bound to peptide PA1, structure B Deposited 2026-05-09 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 389–607（219 aa）
Not recorded A1DFX peptide PA1-A × 1 SO4 SULFATE ION × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291.15 K；0.2 M NH4F and 2.4 M (NH4)2SO4
Resolution 1.52 Å R-free 0.222
13JK E. coli DnaK bound to peptide PA5 Deposited 2026-05-09 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 389–607（219 aa）
Not recorded A1DHT peptide PA5 × 1 IOD IODIDE ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291.15 K；0.2 M NH4I, 2.2 M (NH4)2SO4
Resolution 2.62 Å R-free 0.284
13JK E. coli DnaK bound to peptide PA5 Deposited 2026-05-09 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 389–607（219 aa）
Not recorded A1DHT peptide PA5 × 1 IOD IODIDE ION × 8 SO4 SULFATE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291.15 K；0.2 M NH4I, 2.2 M (NH4)2SO4
Resolution 2.62 Å R-free 0.284

4 other PDB entries and 6 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name DNAK_ECO57
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–219； UniProt 389–607

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.

SAXS scattering curve SAXS Profile

SAXS profile for 13iu

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 13iu
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2. Structure Basics 2. Structure Basics

Entry ID entry_id13iu
Deposition date deposition_date2026-05-08
最后修订 last_revision2026-05-27
Structure title titleE. coli DnaK bound to peptide PA9
Keywords keywordsallosteric inhibition, DnaK, molecular chaperones, peptidomimetics, proteotoxic stress, CHAPERONE; CHAPERONE
Experimental Method methodX-RAY DIFFRACTION
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier21.36 Å
Radius of gyration Rg (electron density) rg_electron20.94 Å
Forward intensity I(0) i019638900.00
Molecular weight molecular_weight22107.0 kDa
Excluded volume excluded_volume21112 ų
Envelope volume envelope_volume37366 ų
Hydration-shell volume shell_volume16060 ų
Envelope diameter envelope_diameter81.7 Å
Shell Rg shell_rg25.93 Å
Envelope Rg envelope_rg21.20 Å
Shape Rg shape_rg20.93 Å
Total Rg total_rg21.49 Å
Total atoms total_atoms1671
Residues n_residues218
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax76.9 Å
Rg (real space) rg_real21.50 Å
Rg uncertainty (real space) rg_real_error0.82 Å
I(0) (real space) i0_real1.9640e+07
I(0) uncertainty (real space) i0_real_error2.6850e+05
Rg (reciprocal space) rg_reciprocal21.47 Å
I(0) (reciprocal space) i0_reciprocal19640000.0000
Solution quality estimate total_estimate0.7599
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks3
Primary peak position r_peak_primary21.5 Å
Skewness Skewness skewness0.478
Kurtosis Kurtosis kurtosis-0.212
Angular range angular_range— – 0.3700 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha3462000.0000
Real-space data points n_real_points69
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.727; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.693; Smooth: 0.000
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

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8. Citations (1)

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9. Files and Curves (10)