SAXSdb — 4ch9

▼

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

KELCH-LIKE PROTEIN 3

HOMO SAPIENS

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 heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain B； UniProt 298–587	Fragment：KELCH DOMAIN, RESIDUES 298-587	SERINE/THREONINE-PROTEIN KINASE WNK4 × 1 （Q96J92） SO4 SULFATE ION × 2 EDO 1,2-ETHANEDIOL × 1 CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 4.3；293 K；SITTING-DROP VAPOUR-DIFFUSTION, 25-35 % PEG 4000, 0.2 M AMMONIUM SULPHATE, 0.1 M ACETATE (PH 4.3), 293 K	Resolution 1.84 Å R-free 0.184
2	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 298–587	Fragment：KELCH DOMAIN, RESIDUES 298-587	SERINE/THREONINE-PROTEIN KINASE WNK4 × 1 （Q96J92） SO4 SULFATE ION × 1 EDO 1,2-ETHANEDIOL × 1 CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 4.3；293 K；SITTING-DROP VAPOUR-DIFFUSTION, 25-35 % PEG 4000, 0.2 M AMMONIUM SULPHATE, 0.1 M ACETATE (PH 4.3), 293 K	Resolution 1.84 Å R-free 0.184

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 4CH9	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
4HXI Crystal structure of KLHL3/Cul3 complex Deposited 2012-11-10	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 24–276（253 aa） Fragment：BTB-BACK	Mutation：K87A, K89A, K90A	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；0.2M ammonium tartrate, 14% PEG 3350, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K	Resolution 3.51 Å R-free 0.278
5NKP Crystal structure of the human KLHL3 Kelch domain in complex with a WNK3 peptide Deposited 2017-03-31	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 298–587（290 aa） Fragment：UNP residues 298-587	Not recorded	CIT CITRIC ACID × 1 CL CHLORIDE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277 K；6% PEG4K -- 0.1M acetate pH 5.1	Resolution 2.80 Å R-free 0.247
5NKP Crystal structure of the human KLHL3 Kelch domain in complex with a WNK3 peptide Deposited 2017-03-31	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 298–587（290 aa） Fragment：UNP residues 298-587	Not recorded	CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277 K；6% PEG4K -- 0.1M acetate pH 5.1	Resolution 2.80 Å R-free 0.247

2 other PDB entries and 3 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	KLHL3_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 3–292； UniProt 298–587 Author chain B； PDBConstruct 3–292； UniProt 298–587

SERINE/THREONINE-PROTEIN KINASE WNK4

OrganismNot specified

UniProt Q96J92

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 heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain D； UniProt 557–567	Fragment：RESIDUES 557-567	KELCH-LIKE PROTEIN 3 × 1 （Q9UH77） SO4 SULFATE ION × 2 EDO 1,2-ETHANEDIOL × 1 CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 4.3；293 K；SITTING-DROP VAPOUR-DIFFUSTION, 25-35 % PEG 4000, 0.2 M AMMONIUM SULPHATE, 0.1 M ACETATE (PH 4.3), 293 K	Resolution 1.84 Å R-free 0.184
2	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain C； UniProt 557–567	Fragment：RESIDUES 557-567	KELCH-LIKE PROTEIN 3 × 1 （Q9UH77） SO4 SULFATE ION × 1 EDO 1,2-ETHANEDIOL × 1 CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 4.3；293 K；SITTING-DROP VAPOUR-DIFFUSTION, 25-35 % PEG 4000, 0.2 M AMMONIUM SULPHATE, 0.1 M ACETATE (PH 4.3), 293 K	Resolution 1.84 Å R-free 0.184

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 4CH9	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
2V3S Structural insights into the recognition of substrates and activators by the OSR1 kinase Deposited 2007-06-21	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 1015–1020（6 aa） Fragment：RESIDUES 1015-1020	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 1.70 Å R-free 0.239
2V3S Structural insights into the recognition of substrates and activators by the OSR1 kinase Deposited 2007-06-21	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain C 1015–1020（6 aa） Fragment：RESIDUES 1015-1020	Not recorded	ACT ACETATE ION × 1	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 1.70 Å R-free 0.239
4CHB Crystal structure of the human KLHL2 Kelch domain in complex with a WNK4 peptide Deposited 2013-11-29	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain C 557–567（11 aa） Fragment：RESIDUES 557-567	Not recorded	EDO 1,2-ETHANEDIOL × 3 SO4 SULFATE ION × 2 12P DODECAETHYLENE GLYCOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.2；293 K；SITTING-DROP VAPOUR-DIFFUSION, 2.5 M AMMONIUM SULPHATE, 0.1 M HEPES, 2 % PEG 400 (PH 7.2), 293 K	Resolution 1.56 Å R-free 0.194
4CHB Crystal structure of the human KLHL2 Kelch domain in complex with a WNK4 peptide Deposited 2013-11-29	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 557–567（11 aa） Fragment：RESIDUES 557-567	Not recorded	EDO 1,2-ETHANEDIOL × 3 SO4 SULFATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.2；293 K；SITTING-DROP VAPOUR-DIFFUSION, 2.5 M AMMONIUM SULPHATE, 0.1 M HEPES, 2 % PEG 400 (PH 7.2), 293 K	Resolution 1.56 Å R-free 0.194

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

View Construct and Data Evidence

UniProt name	WNK4_HUMAN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain C； PDBConstruct 1–11； UniProt 557–567 Author chain D； PDBConstruct 1–11； UniProt 557–567

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.

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id	4ch9
Deposition date deposition_date	2013-11-29
Structure title title	Crystal structure of the human KLHL3 Kelch domain in complex with a WNK4 peptide
Keywords keywords	SIGNALING PROTEIN-TRANSFERASE COMPLEX, KLHL3, UBIQUITIN, ADAPTOR PROTEIN, PROTEIN-BINDING, KELCH REPEAT, WNK SIGNALLING PATHWAY; SIGNALING PROTEIN/TRANSFERASE
Experimental Method method	X-RAY DIFFRACTION

▼

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

Radius of gyration Rg (Guinier) rg_guinier	26.74 Å
Radius of gyration Rg (electron density) rg_electron	26.48 Å
Forward intensity I(0) i0	71254700.00
Molecular weight molecular_weight	63468.0 kDa
Excluded volume excluded_volume	78231 Å³
Envelope volume envelope_volume	92160 Å³
Hydration-shell volume shell_volume	29277 Å³
Envelope diameter envelope_diameter	92.4 Å
Shell Rg shell_rg	33.37 Å
Envelope Rg envelope_rg	26.56 Å
Shape Rg shape_rg	26.53 Å
Total Rg total_rg	27.04 Å
Total atoms total_atoms	4452
Residues n_residues	590
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

▼

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

Maximum dimension Dmax dmax	88.3 Å
Rg (real space) rg_real	26.80 Å
Rg uncertainty (real space) rg_real_error	0.70 Å
I(0) (real space) i0_real	7.1250e+07
I(0) uncertainty (real space) i0_real_error	1.0540e+06
Rg (reciprocal space) rg_reciprocal	26.79 Å
I(0) (reciprocal space) i0_reciprocal	71250000.0000
Solution quality estimate total_estimate	0.7981
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	29.9 Å
Skewness Skewness skewness	0.413
Kurtosis Kurtosis kurtosis	-0.387
Angular range angular_range	— – 0.2950 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	13550000.0000
Real-space data points n_real_points	60
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.810; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.941; Smooth: 0.000

▶

5. Crystallography and Experiment 5. Crystallography & Experiment

▶

6. Entities and Polymers Entities & Polymers (6)

Entity 1 Entity 1 polymer

Description description	KELCH-LIKE PROTEIN 3
Molecular weight formula_weight	31529.5 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	5096

SMSLPKVMIVVGGQAPKAIRSVECYDFEEDRWDQIAELPSRRCRAGVVFMAGHVYAVGGFNGSLRVRTVDVYDGVKDQWTSIASMQERRSTLGAAVLNDLLYAVGGFDGSTGLASVEAYSYKTNEWFFVAPMNTRRSSVGVGVVEGKLYAVGGYDGASRQCLSTVEQYNPATNEWIYVADMSTRRSGAGVGVLSGQLYATGGHDGPLVRKSVEVYDPGTNTWKQVADMNMCRRNAGVCAVNGLLYVVGGDDGSCNLASVEYYNPVTDKWTLLPTNMSTGRSYAGVAVIHKSL

来源 Source

来源生物 organism	HOMO SAPIENS
通用名 common_name	HUMAN
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	ESCHERICHIA COLI

Entity 2 Entity 2 polymer

Description description	SERINE/THREONINE-PROTEIN KINASE WNK4
Molecular weight formula_weight	1309.3 kDa
EC 编号 ec_number	2.7.11.1
Source method src_method	syn
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C,D

EPEEPEADQHQ

Entity 3 Entity 3 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 4 Entity 4 non-polymer

Description description	1,2-ETHANEDIOL
Molecular weight formula_weight	62.1 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 5 Entity 5 non-polymer

Description description	CHLORIDE ION
Molecular weight formula_weight	35.5 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 6 Entity 6 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	577

▼

7. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id	4ch9A00
Class class	2 — Mainly Beta
Architecture architecture	120 — 6 Propeller
Topology topology	10 — Neuraminidase
Homologous superfamily homologous superfamily	80 — Kelch-type beta propeller

Domain ID domain_id	4ch9B00
Class class	2 — Mainly Beta
Architecture architecture	120 — 6 Propeller
Topology topology	10 — Neuraminidase
Homologous superfamily homologous superfamily	80 — Kelch-type beta propeller

▶

8. Citations (1)

▶

Unit-cell length a length_a	45.330 Å
Unit-cell length b length_b	84.760 Å
Unit-cell length c length_c	146.790 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 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	1.840 Å
Low-resolution limit resolution_low	73.402 Å
R factor r_factor	0.1459
R_work r_work	0.1439
R_free r_free	0.1840

fit	/app/data/saxs_computation/ch/4ch9/4ch9.fit
pddf	/app/data/pr_computation/ch/4ch9/4ch9.pr.out
profile	/app/data/saxs_computation/ch/4ch9/4ch9.dat

Crystal structure of the human KLHL3 Kelch domain in complex with a WNK4 peptide

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

KELCH-LIKE PROTEIN 3

State in the Current Structure

Other States of the Same Protein in the Database

SERINE/THREONINE-PROTEIN KINASE WNK4

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

6. Entities and Polymers Entities & Polymers (6)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 water

7. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)