SAXSdb — 13iv

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1. Protein Identity and Related Structures Protein Identity & Related Structures

Chaperone protein DnaK

Escherichia coli

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	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
2	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain B； UniProt 389–607	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

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 13IV	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
13IU E. coli DnaK bound to peptide PA9 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	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
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 5 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 Author chain B； 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.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	13iv
Deposition date deposition_date	2026-05-08
最后修订 last_revision	2026-05-27
Structure title title	E. coli DaK bound to peptide PA1, structure A
Keywords keywords	allosteric inhibition, DnaK, molecular chaperones, peptidomimetics, proteotoxic stress, CHAPERONE; CHAPERONE
Experimental Method method	X-RAY DIFFRACTION

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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	23.73 Å
Radius of gyration Rg (electron density) rg_electron	22.96 Å
Forward intensity I(0) i0	73420300.00
Molecular weight molecular_weight	43665.0 kDa
Excluded volume excluded_volume	41651 Å³
Envelope volume envelope_volume	74417 Å³
Hydration-shell volume shell_volume	27013 Å³
Envelope diameter envelope_diameter	82.1 Å
Shell Rg shell_rg	30.10 Å
Envelope Rg envelope_rg	22.93 Å
Shape Rg shape_rg	22.96 Å
Total Rg total_rg	23.59 Å
Total atoms total_atoms	3298
Residues n_residues	434
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	71.1 Å
Rg (real space) rg_real	23.68 Å
Rg uncertainty (real space) rg_real_error	0.12 Å
I(0) (real space) i0_real	7.1280e+07
I(0) uncertainty (real space) i0_real_error	7.2890e+05
Rg (reciprocal space) rg_reciprocal	23.62 Å
I(0) (reciprocal space) i0_reciprocal	73420000.0000
Solution quality estimate total_estimate	0.7108
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	31.1 Å
Skewness Skewness skewness	0.165
Kurtosis Kurtosis kurtosis	-0.398
Angular range angular_range	— – 0.3350 Å⁻¹
Current regularization parameter α current_alpha	7.5490
Highest regularization parameter α highest_alpha	8733000.0000
Real-space data points n_real_points	65
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.956; Stabil: 0.924; Sysdev: 0.000; Positv: 1.000; Valcen: 0.990; Smooth: 0.631

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	Chaperone protein DnaK
Molecular weight formula_weight	23820.8 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	3319

VLLLDVTPLSLGIETMGGVMTTLIAKNTTIPTKHSQVFSTAEDNQSAVTIHVLQGERKRAADNKSLGQFNLDGINPAPRGMPQIEVTFDIDADGILHVSAKDKNSGKEQKITIKASSGLNEDEIQKMVRDAEANAEADRKFEELVQTRNQGDHLLHSTRKQVEEAGDKLPADDKTAIESALTALETALKGEDKAAIEAKMQELAQVSQKLMEIAQQQHA

来源 Source

来源生物 organism	Escherichia coli
NCBI Class编号 ncbi_taxonomy_id	562
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	peptide PA1-A
Molecular weight formula_weight	745.9 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	13

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8. Citations (1)

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Unit-cell length a length_a	98.532 Å
Unit-cell length b length_b	115.895 Å
Unit-cell length c length_c	37.752 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

Space group space_group	P 21 21 2
Space-group number int_tables_number	18
Crystal system crystal_system	orthorhombic

Resolution resolution	3.230 Å
Low-resolution limit resolution_low	31.630 Å
R factor r_factor	0.2519
R_work r_work	0.2495
R_free r_free	0.2961

fit	/app/data/saxs_computation/3i/13iv/13iv.fit
pddf	/app/data/pr_computation/3i/13iv/13iv.pr.out
profile	/app/data/saxs_computation/3i/13iv/13iv.dat

E. coli DaK bound to peptide PA1, structure A

1. Protein Identity and Related Structures Protein Identity & Related Structures

Chaperone protein DnaK

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction