5wc5

Structural insights into the potency of SK/IK channel positive modulators

Method: X-RAY DIFFRACTION Dmax: 83.2 Å Quality: GOOD

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

Small conductance calcium-activated potassium channel protein 2

Homo sapiens

UniProt Q9H2S1

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 395–486 Mutation:N407A Calmodulin-1 × 1 (P0DP23) SO4 SULFATE ION × 6 GOL GLYCEROL × 1 CA CALCIUM ION × 2 AJV 7-fluoro-3-(hydroxyamino)-2H-indol-2-one × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 5.8;293.15 K;0.1 M Sodium citrate tribasic dihydrate 0.5 M Ammonium sulfate 1.5 M Litium sulfate monohydrate Resolution 2.30 Å R-free 0.250
2 Protein heterocomplex Heteromer Protein × 4 PDB declaration: tetrameric(4) Consistent with protein copy count Chain B; UniProt 395–486 Mutation:N407A Calmodulin-1 × 2 (P0DP23) SO4 SULFATE ION × 12 GOL GLYCEROL × 2 CA CALCIUM ION × 4 AJV 7-fluoro-3-(hydroxyamino)-2H-indol-2-one × 2 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 5.8;293.15 K;0.1 M Sodium citrate tribasic dihydrate 0.5 M Ammonium sulfate 1.5 M Litium sulfate monohydrate Resolution 2.30 Å R-free 0.250

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.

15 other PDB entries and 16 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name KCNN2_HUMAN
Isoform
PDB entities 1
Chains and sequence ranges Author chain B; PDBConstruct 2–93; UniProt 395–486

Calmodulin-1

Homo sapiens

UniProt P0DP23

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 R; UniProt 5–148 Not recorded Small conductance calcium-activated potassium channel protein 2 × 1 (Q9H2S1) SO4 SULFATE ION × 6 GOL GLYCEROL × 1 CA CALCIUM ION × 2 AJV 7-fluoro-3-(hydroxyamino)-2H-indol-2-one × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 5.8;293.15 K;0.1 M Sodium citrate tribasic dihydrate 0.5 M Ammonium sulfate 1.5 M Litium sulfate monohydrate Resolution 2.30 Å R-free 0.250
2 Protein heterocomplex Heteromer Protein × 4 PDB declaration: tetrameric(4) Consistent with protein copy count Chain R; UniProt 5–148 Not recorded Small conductance calcium-activated potassium channel protein 2 × 2 (Q9H2S1) SO4 SULFATE ION × 12 GOL GLYCEROL × 2 CA CALCIUM ION × 4 AJV 7-fluoro-3-(hydroxyamino)-2H-indol-2-one × 2 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 5.8;293.15 K;0.1 M Sodium citrate tribasic dihydrate 0.5 M Ammonium sulfate 1.5 M Litium sulfate monohydrate Resolution 2.30 Å R-free 0.250

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.

213 other PDB entries and 278 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name CALM1_HUMAN
Isoform
PDB entities 2
Chains and sequence ranges Author chain R; PDBConstruct 3–146; UniProt 5–148

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 5wc5

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 5wc5
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2. Structure Basics 2. Structure Basics

Entry ID entry_id5wc5
Deposition date deposition_date2017-06-29
Structure title titleStructural insights into the potency of SK/IK channel positive modulators
Keywords keywordsCalcium binding protein, METAL TRANSPORT; METAL TRANSPORT
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier25.53
Radius of gyration Rg (electron density) rg_electron24.97
Forward intensity I(0) i015949700.00
Molecular weight molecular_weight28503.0 kDa
Excluded volume excluded_volume34952 ų
Envelope volume envelope_volume47789 ų
Hydration-shell volume shell_volume17609 ų
Envelope diameter envelope_diameter89.3
Shell Rg shell_rg29.01
Envelope Rg envelope_rg24.87
Shape Rg shape_rg24.94
Total Rg total_rg25.58
Total atoms total_atoms1982
Residues n_residues241
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 dmax83.2
Rg (real space) rg_real25.62
Rg uncertainty (real space) rg_real_error0.94
I(0) (real space) i0_real1.5950e+07
I(0) uncertainty (real space) i0_real_error2.7350e+05
Rg (reciprocal space) rg_reciprocal25.59
I(0) (reciprocal space) i0_reciprocal15950000.0000
Solution quality estimate total_estimate0.8118
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary21.5
Skewness Skewness skewness0.296
Kurtosis Kurtosis kurtosis-0.644
Angular range angular_range— – 0.3100 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha1260000.0000
Real-space data points n_real_points63
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.907; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.830; Smooth: 0.000

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (7)

7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_idd5wc5r1
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
Domain ID domain_idd5wc5r2
Class classl — Artifacts
Fold Fold foldl.1 — Tags
Superfamily Superfamily superfamilyl.1.1 — Tags
Family Family familyl.1.1.1 — Tags

CATH v4.4 (2 domains)

Domain ID domain_id5wc5B00
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology287 — Helix Hairpins
Homologous superfamily homologous superfamily70
Domain ID domain_id5wc5R01
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)