1yr5

1.7-A structure of calmodulin bound to a peptide from DAP kinase

Method: X-RAY DIFFRACTION Dmax: 57.5 Å Quality: GOOD

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

calmodulin

Homo sapiens

UniProt P62158

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 A; UniProt 1–148 Fragment:residues 1-148 19-mer from Death-associated protein kinase 1 × 1 (P53355) CA CALCIUM ION × 4 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 4.8;295 K;PEG 8000, sodium acetate, calcium chloride, pH 4.8, VAPOR DIFFUSION, HANGING DROP, temperature 295K Resolution 1.70 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.

105 other PDB entries and 176 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name CALM_HUMAN
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 1–148; UniProt 1–148

19-mer from Death-associated protein kinase 1

OrganismNot specified

UniProt P53355

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 302–320 Not recorded calmodulin × 1 (P62158) CA CALCIUM ION × 4 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 4.8;295 K;PEG 8000, sodium acetate, calcium chloride, pH 4.8, VAPOR DIFFUSION, HANGING DROP, temperature 295K Resolution 1.70 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.

77 other PDB entries and 81 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name DAPK1_HUMAN
Isoform
PDB entities 2
Chains and sequence ranges Author chain B; PDBConstruct 1–19; UniProt 302–320

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 1yr5

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 1yr5
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2. Structure Basics 2. Structure Basics

Entry ID entry_id1yr5
Deposition date deposition_date2005-02-03
Structure title title1.7-A structure of calmodulin bound to a peptide from DAP kinase
Keywords keywordsEF hand, METAL BINDING PROTEIN-TRANSFERASE COMPLEX; METAL BINDING PROTEIN/TRANSFERASE
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier17.34
Radius of gyration Rg (electron density) rg_electron16.03
Forward intensity I(0) i07583140.00
Molecular weight molecular_weight19050.0 kDa
Excluded volume excluded_volume23413 ų
Envelope volume envelope_volume27096 ų
Hydration-shell volume shell_volume14524 ų
Envelope diameter envelope_diameter55.3
Shell Rg shell_rg21.55
Envelope Rg envelope_rg16.15
Shape Rg shape_rg16.05
Total Rg total_rg16.95
Total atoms total_atoms1324
Residues n_residues165
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 dmax57.5
Rg (real space) rg_real17.27
Rg uncertainty (real space) rg_real_error0.36
I(0) (real space) i0_real7.5830e+06
I(0) uncertainty (real space) i0_real_error8.9820e+04
Rg (reciprocal space) rg_reciprocal17.28
I(0) (reciprocal space) i0_reciprocal7583000.0000
Solution quality estimate total_estimate0.8063
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks3
Primary peak position r_peak_primary21.2
Skewness Skewness skewness0.225
Kurtosis Kurtosis kurtosis-0.359
Angular range angular_range— – 0.4600 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha1065000.0000
Real-space data points n_real_points77
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.826; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.000

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (4)

7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_idd1yr5a_
Class classa — All alpha proteins
Fold Fold folda.39 — EF Hand-like
Superfamily Superfamily superfamilya.39.1 — EF-hand
Family Family familya.39.1.5 — Calmodulin-like

CATH v4.4 (1 domains)

Domain ID domain_id1yr5A00
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology238 — Recoverin; domain 1
Homologous superfamily homologous superfamily10 — EF-hand

8. Citations (1)

9. Files and Curves (10)