SAXSdb — 1bhd

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

UTROPHIN

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 144–261	Fragment：2ND CALPONIN HOMOLOGY DOMAIN FROM ACTIN BINDING REGION	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：pH 7.6；pH 7.6	Resolution 2.00 Å R-free 0.257
2	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain B； UniProt 144–261	Fragment：2ND CALPONIN HOMOLOGY DOMAIN FROM ACTIN BINDING REGION	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：pH 7.6；pH 7.6	Resolution 2.00 Å R-free 0.257

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 1BHD	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1QAG Actin binding region of the dystrophin homologue utrophin Deposited 1999-03-05	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 31–256（226 aa） Fragment：RESIDUES 28-261	Mutation：SELENOMETHIONINE REPLACES METHIONINE Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；293 K；0.1M Sodium Acetate pH 4.7, 2.0 M unbuffered sodium formate., pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 3.00 Å R-free 0.258
1QAG Actin binding region of the dystrophin homologue utrophin Deposited 1999-03-05	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 31–256（226 aa） Fragment：RESIDUES 28-261	Mutation：SELENOMETHIONINE REPLACES METHIONINE Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；293 K；0.1M Sodium Acetate pH 4.7, 2.0 M unbuffered sodium formate., pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 3.00 Å R-free 0.258
1QAG Actin binding region of the dystrophin homologue utrophin Deposited 1999-03-05	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 3 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 31–256（226 aa） Fragment：RESIDUES 28-261 Chain B 31–256（226 aa） Fragment：RESIDUES 28-261	Mutation：SELENOMETHIONINE REPLACES METHIONINE Non-standard monomer：Yes (specific site not provided by mmCIF) Mutation：SELENOMETHIONINE REPLACES METHIONINE Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；293 K；0.1M Sodium Acetate pH 4.7, 2.0 M unbuffered sodium formate., pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 3.00 Å R-free 0.258
6M5G F-actin-Utrophin complex Deposited 2020-03-10	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric	Chain F 1–261（261 aa） Fragment：calponin domain 1, calponin domain 2 Chain G 1–261（261 aa） Fragment：calponin domain 1, calponin domain 2 Chain H 1–261（261 aa） Fragment：calponin domain 1, calponin domain 2	Not recorded	MG MAGNESIUM ION × 5 ADP ADENOSINE-5'-DIPHOSPHATE × 5	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE；blot for 3 seconds	Resolution 3.60 Å

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

View Construct and Data Evidence

UniProt name	UTRO_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–118； UniProt 144–261 Author chain B； PDBConstruct 1–118； UniProt 144–261

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	1bhd
Deposition date deposition_date	1998-06-05
Structure title title	SECOND CALPONIN HOMOLOGY DOMAIN FROM UTROPHIN
Keywords keywords	CALPONIN HOMOLOGY, ACTIN BINDING, STRUCTURAL PROTEIN; STRUCTURAL PROTEIN
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	29.68 Å
Radius of gyration Rg (electron density) rg_electron	29.19 Å
Forward intensity I(0) i0	9342850.00
Molecular weight molecular_weight	25045.0 kDa
Excluded volume excluded_volume	31942 Å³
Envelope volume envelope_volume	43691 Å³
Hydration-shell volume shell_volume	12431 Å³
Envelope diameter envelope_diameter	89.5 Å
Shell Rg shell_rg	36.61 Å
Envelope Rg envelope_rg	28.04 Å
Shape Rg shape_rg	29.19 Å
Total Rg total_rg	30.07 Å
Total atoms total_atoms	1771
Residues n_residues	216
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	89.8 Å
Rg (real space) rg_real	29.96 Å
Rg uncertainty (real space) rg_real_error	0.92 Å
I(0) (real space) i0_real	9.3430e+06
I(0) uncertainty (real space) i0_real_error	1.6050e+05
Rg (reciprocal space) rg_reciprocal	29.85 Å
I(0) (reciprocal space) i0_reciprocal	9342000.0000
Solution quality estimate total_estimate	0.6208
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	3
Primary peak position r_peak_primary	18.6 Å
Skewness Skewness skewness	0.197
Kurtosis Kurtosis kurtosis	-1.348
Angular range angular_range	— – 0.2650 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	5343000.0000
Real-space data points n_real_points	54
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.017; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.118; Smooth: 0.900

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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) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d1bhda_
Class class	a — All alpha proteins
Fold Fold fold	a.40 — CH domain-like
Superfamily Superfamily superfamily	a.40.1 — Calponin-homology domain, CH-domain
Family Family family	a.40.1.1 — Calponin-homology domain, CH-domain

Domain ID domain_id	d1bhdb_
Class class	a — All alpha proteins
Fold Fold fold	a.40 — CH domain-like
Superfamily Superfamily superfamily	a.40.1 — Calponin-homology domain, CH-domain
Family Family family	a.40.1.1 — Calponin-homology domain, CH-domain

CATH v4.4 (2 domains)

Domain ID domain_id	1bhdA00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	418 — Actin-binding Protein, T-fimbrin; domain 1
Homologous superfamily homologous superfamily	10 — Calponin-like domain

Domain ID domain_id	1bhdB00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	418 — Actin-binding Protein, T-fimbrin; domain 1
Homologous superfamily homologous superfamily	10 — Calponin-like domain

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8. Citations (1)

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Unit-cell length a length_a	63.920 Å
Unit-cell length b length_b	32.210 Å
Unit-cell length c length_c	65.360 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	116.25 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	2.000 Å
Low-resolution limit resolution_low	20.000 Å
R factor r_factor	0.2020
R_work r_work	0.1850
R_free r_free	0.2570

Description description	UTROPHIN
Molecular weight formula_weight	13678.7 kDa
Source method src_method	man
Copy count entity_count	2

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	1944

SECOND CALPONIN HOMOLOGY DOMAIN FROM UTROPHIN

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

UTROPHIN

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) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (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 BL21(DE3)

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	173

fit	/app/data/saxs_computation/bh/1bhd/1bhd.fit
pddf	/app/data/pr_computation/bh/1bhd/1bhd.pr.out
profile	/app/data/saxs_computation/bh/1bhd/1bhd.dat