SAXSdb — 7kpi

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

Speckle-type POZ protein

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 monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain A； UniProt 28–166	Not recorded	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；298 K；0.1 M HEPES, pH 7.5, 23% (w/v) PME 550, 5 mM DTT	Resolution 1.70 Å R-free 0.196

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 7KPI	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
7KPK Crystal structure of the SPOP MATH domain in complex with a fragment of Pdx1 Deposited 2020-11-11	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 28–166（139 aa） Fragment：MATH domain	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；295 K；50 mM sodium cacodylate, pH 6.5, 0.08 M magnesium acetate, 30% (w/v) PEG 4000	Resolution 1.71 Å R-free 0.227
9HFU Caprin1 peptide bound to SPOP MATH domain Deposited 2024-11-18	Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 28–166（139 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；12.5% w/v PEG 1000, 12.5% w/v PEG 3350, 12.5% v/v MPD, 0.03 M sodium fluoride, 0.03 M sodium bromide, 0.03 M sodium iodide, 0.1 M bicine/Trizma base pH 8.5	Resolution 1.70 Å R-free 0.204
9HFU Caprin1 peptide bound to SPOP MATH domain Deposited 2024-11-18	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 28–166（139 aa）	Not recorded	NA SODIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；12.5% w/v PEG 1000, 12.5% w/v PEG 3350, 12.5% v/v MPD, 0.03 M sodium fluoride, 0.03 M sodium bromide, 0.03 M sodium iodide, 0.1 M bicine/Trizma base pH 8.5	Resolution 1.70 Å R-free 0.204
9HFW SRC-3 (NCoA-3) peptide bound to SPOP MATH domain Deposited 2024-11-18	Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 28–166（139 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；12.5% w/v PEG 1000, 12.5% w/v PEG 3350, 12.5% v/v MPD, 0.03 M sodium fluoride, 0.03 M sodium bromide, 0.03 M sodium iodide, 0.1 M bicine/Trizma base pH 8.5	Resolution 1.70 Å R-free 0.223
9HGH MyD88 peptide_1 bound to SPOP MATH domain Deposited 2024-11-19	Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 28–166（139 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；12.5% w/v PEG 1000, 12.5% w/v PEG 3350, 12.5% v/v MPD, 0.03 M diethyleneglycol, 0.03 M triethyleneglycol, 0.03 M tetraethyleneglycol, 0.03 M pentaethyleneglycol, 0.1 M bicine/Trizma base pH 8.5	Resolution 1.90 Å R-free 0.232

4 other PDB entries and 5 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	D6RDG8_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 4–142； UniProt 28–166

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	7kpi
Deposition date deposition_date	2020-11-11
Structure title title	Crystal structure of the SPOP MATH domain
Keywords keywords	ubiquitin, ligase, adaptor, protein, GENE REGULATION; GENE REGULATION
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	16.74 Å
Radius of gyration Rg (electron density) rg_electron	15.41 Å
Forward intensity I(0) i0	4733550.00
Molecular weight molecular_weight	16145.0 kDa
Excluded volume excluded_volume	20442 Å³
Envelope volume envelope_volume	23054 Å³
Hydration-shell volume shell_volume	12949 Å³
Envelope diameter envelope_diameter	53.9 Å
Shell Rg shell_rg	20.96 Å
Envelope Rg envelope_rg	15.86 Å
Shape Rg shape_rg	15.36 Å
Total Rg total_rg	16.62 Å
Total atoms total_atoms	1136
Residues n_residues	140
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	55.4 Å
Rg (real space) rg_real	16.70 Å
Rg uncertainty (real space) rg_real_error	0.33 Å
I(0) (real space) i0_real	4.7340e+06
I(0) uncertainty (real space) i0_real_error	6.0550e+04
Rg (reciprocal space) rg_reciprocal	16.71 Å
I(0) (reciprocal space) i0_reciprocal	4734000.0000
Solution quality estimate total_estimate	0.6422
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	19.4 Å
Skewness Skewness skewness	0.271
Kurtosis Kurtosis kurtosis	-0.331
Angular range angular_range	— – 0.4750 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	739700.0000
Real-space data points n_real_points	78
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.843; Stabil: 1.000; Sysdev: 0.272; Positv: 1.000; Valcen: 0.999; Smooth: 0.000

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (2)

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7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d7kpia1
Class class	b — All beta proteins
Fold Fold fold	b.8 — TRAF domain-like
Superfamily Superfamily superfamily	b.8.1 — TRAF domain-like
Family Family family	b.8.1.1 — MATH domain

Domain ID domain_id	d7kpia2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

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8. Citations (1)

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Unit-cell length a length_a	62.642 Å
Unit-cell length b length_b	53.246 Å
Unit-cell length c length_c	41.596 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	101.39 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

Space group space_group	C 1 2 1
Space-group number int_tables_number	5
Crystal system crystal_system	monoclinic

Resolution resolution	1.700 Å
Low-resolution limit resolution_low	40.780 Å
R factor r_factor	0.1611
R_work r_work	0.1592
R_free r_free	0.1957

Description description	Speckle-type POZ protein
Molecular weight formula_weight	16352.8 kDa
Source method src_method	man
Copy count entity_count	1

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	1335

Crystal structure of the SPOP MATH domain

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

Speckle-type POZ protein

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 (2)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 water

7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (2 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)

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

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	146

fit	/app/data/saxs_computation/kp/7kpi/7kpi.fit
pddf	/app/data/pr_computation/kp/7kpi/7kpi.pr.out
profile	/app/data/saxs_computation/kp/7kpi/7kpi.dat