1dxx

N-terminal Actin-binding Domain of Human Dystrophin

Method: X-RAY DIFFRACTION Dmax: 106.9 Å Quality: EXCELLENT

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

DYSTROPHIN

HOMO SAPIENS

UniProt P11532

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 homooligomer Homooligomer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain A; UniProt 1–246 Chain B; UniProt 1–246 Fragment:ACTIN-BINDING Mutation:YES No other associated polymer X-RAY DIFFRACTION X-ray crystallization conditions:pH 7.4;1.55M AMMONIUM FORMATE, 0.1M HEPES 7.4, pH 7.40 Resolution 2.60 Å R-free 0.268
2 Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain C; UniProt 1–246 Chain D; UniProt 1–246 Fragment:ACTIN-BINDING Mutation:YES No other associated polymer X-RAY DIFFRACTION X-ray crystallization conditions:pH 7.4;1.55M AMMONIUM FORMATE, 0.1M HEPES 7.4, pH 7.40 Resolution 2.60 Å R-free 0.268

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.

5 other PDB entries and 17 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name DMD_HUMAN
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 1–246; UniProt 1–246 Author chain B; PDBConstruct 1–246; UniProt 1–246 Author chain C; PDBConstruct 1–246; UniProt 1–246 Author chain D; PDBConstruct 1–246; UniProt 1–246

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 1dxx

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 1dxx
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2. Structure Basics 2. Structure Basics

Entry ID entry_id1dxx
Deposition date deposition_date2000-01-20
Structure title titleN-terminal Actin-binding Domain of Human Dystrophin
Keywords keywordsSTRUCTURAL PROTEIN, DYSTROPHIN, MUSCULAR DYSTROPHY, CALPONIN HOMOLOGY DOMAIN, ACTIN-BINDING, UTROPHIN; STRUCTURAL PROTEIN
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier35.74
Radius of gyration Rg (electron density) rg_electron34.51
Forward intensity I(0) i0174278000.00
Molecular weight molecular_weight106820.0 kDa
Excluded volume excluded_volume134100 ų
Envelope volume envelope_volume175570 ų
Hydration-shell volume shell_volume41468 ų
Envelope diameter envelope_diameter109.7
Shell Rg shell_rg42.52
Envelope Rg envelope_rg33.26
Shape Rg shape_rg34.54
Total Rg total_rg34.98
Total atoms total_atoms7548
Residues n_residues952
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 −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

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

Maximum dimension Dmax dmax106.9
Rg (real space) rg_real35.49
Rg uncertainty (real space) rg_real_error0.80
I(0) (real space) i0_real1.7430e+08
I(0) uncertainty (real space) i0_real_error2.7980e+06
Rg (reciprocal space) rg_reciprocal35.65
I(0) (reciprocal space) i0_reciprocal174300000.0000
Solution quality estimate total_estimate0.9017
Solution quality rating solution_quality EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary53.5
Skewness Skewness skewness-0.067
Kurtosis Kurtosis kurtosis-0.696
Angular range angular_range— – 0.2200 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha17450000.0000
Real-space data points n_real_points45
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.931; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.993; Smooth: 0.933

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (2)

7. Fold Classification (SCOP + CATH) 16 domains

SCOP 2.08 (8 domains)

Domain ID domain_idd1dxxa1
Class classa — All alpha proteins
Fold Fold folda.40 — CH domain-like
Superfamily Superfamily superfamilya.40.1 — Calponin-homology domain, CH-domain
Family Family familya.40.1.1 — Calponin-homology domain, CH-domain
Domain ID domain_idd1dxxa2
Class classa — All alpha proteins
Fold Fold folda.40 — CH domain-like
Superfamily Superfamily superfamilya.40.1 — Calponin-homology domain, CH-domain
Family Family familya.40.1.1 — Calponin-homology domain, CH-domain
Domain ID domain_idd1dxxb1
Class classa — All alpha proteins
Fold Fold folda.40 — CH domain-like
Superfamily Superfamily superfamilya.40.1 — Calponin-homology domain, CH-domain
Family Family familya.40.1.1 — Calponin-homology domain, CH-domain
Domain ID domain_idd1dxxb2
Class classa — All alpha proteins
Fold Fold folda.40 — CH domain-like
Superfamily Superfamily superfamilya.40.1 — Calponin-homology domain, CH-domain
Family Family familya.40.1.1 — Calponin-homology domain, CH-domain
Domain ID domain_idd1dxxc1
Class classa — All alpha proteins
Fold Fold folda.40 — CH domain-like
Superfamily Superfamily superfamilya.40.1 — Calponin-homology domain, CH-domain
Family Family familya.40.1.1 — Calponin-homology domain, CH-domain
Domain ID domain_idd1dxxc2
Class classa — All alpha proteins
Fold Fold folda.40 — CH domain-like
Superfamily Superfamily superfamilya.40.1 — Calponin-homology domain, CH-domain
Family Family familya.40.1.1 — Calponin-homology domain, CH-domain
Domain ID domain_idd1dxxd1
Class classa — All alpha proteins
Fold Fold folda.40 — CH domain-like
Superfamily Superfamily superfamilya.40.1 — Calponin-homology domain, CH-domain
Family Family familya.40.1.1 — Calponin-homology domain, CH-domain
Domain ID domain_idd1dxxd2
Class classa — All alpha proteins
Fold Fold folda.40 — CH domain-like
Superfamily Superfamily superfamilya.40.1 — Calponin-homology domain, CH-domain
Family Family familya.40.1.1 — Calponin-homology domain, CH-domain

CATH v4.4 (8 domains)

Domain ID domain_id1dxxA01
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology418 — Actin-binding Protein, T-fimbrin; domain 1
Homologous superfamily homologous superfamily10 — Calponin-like domain
Domain ID domain_id1dxxA02
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology418 — Actin-binding Protein, T-fimbrin; domain 1
Homologous superfamily homologous superfamily10 — Calponin-like domain
Domain ID domain_id1dxxB01
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology418 — Actin-binding Protein, T-fimbrin; domain 1
Homologous superfamily homologous superfamily10 — Calponin-like domain
Domain ID domain_id1dxxB02
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology418 — Actin-binding Protein, T-fimbrin; domain 1
Homologous superfamily homologous superfamily10 — Calponin-like domain
Domain ID domain_id1dxxC01
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology418 — Actin-binding Protein, T-fimbrin; domain 1
Homologous superfamily homologous superfamily10 — Calponin-like domain
Domain ID domain_id1dxxC02
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology418 — Actin-binding Protein, T-fimbrin; domain 1
Homologous superfamily homologous superfamily10 — Calponin-like domain
Domain ID domain_id1dxxD01
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology418 — Actin-binding Protein, T-fimbrin; domain 1
Homologous superfamily homologous superfamily10 — Calponin-like domain
Domain ID domain_id1dxxD02
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology418 — Actin-binding Protein, T-fimbrin; domain 1
Homologous superfamily homologous superfamily10 — Calponin-like domain

8. Citations (1)

9. Files and Curves (10)