5xyl

Solution Structure of Skp1 from Homo sapiens

Method: SOLUTION NMR Dmax: 52.5 Å Quality: REASONABLE

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

S-phase kinase-associated protein 1

Homo sapiens

UniProt P63208

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 1–163 Not recorded No other associated polymer SOLUTION NMR NMR measurement conditions:pH 6.5;298 K;Ionic strength (raw mmCIF value) 100;Pressure 1 NMR sample composition:20 mM sodium phosphate, 100 mM sodium chloride, 90% H2O/10% D2O | 90% H2O/10% D2O NMR sample composition:20 mM sodium phosphate, 100 mM sodium chloride, 90% H2O/10% D2O | 90% H2O/10% D2O NMR sample composition:20 mM sodium phosphate, 100 mM sodium chloride, 100% D2O | 100% D2O Resolution not provided

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.

71 other PDB entries and 97 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name SKP1_HUMAN
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 1–163; UniProt 1–163

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 5xyl

P(r) Distance Distribution P(r) Distribution

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

Entry ID entry_id5xyl
Deposition date deposition_date2017-07-09
Structure title titleSolution Structure of Skp1 from Homo sapiens
Keywords keywordsFbox interacting protein, CELL CYCLE; CELL CYCLE
Experimental Method methodSOLUTION NMR

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

Radius of gyration Rg (Guinier) rg_guinier20.20
Radius of gyration Rg (electron density) rg_electron19.61
Forward intensity I(0) i0508229000.00
Molecular weight molecular_weight186400.0 kDa
Excluded volume excluded_volume232180 ų
Envelope volume envelope_volume71867 ų
Hydration-shell volume shell_volume25294 ų
Envelope diameter envelope_diameter95.5
Shell Rg shell_rg30.54
Envelope Rg envelope_rg26.09
Shape Rg shape_rg19.61
Total Rg total_rg20.01
Total atoms total_atoms25910
Residues n_residues1630
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 dmax52.5
Rg (real space) rg_real18.73
Rg uncertainty (real space) rg_real_error0.09
I(0) (real space) i0_real4.8110e+08
I(0) uncertainty (real space) i0_real_error4.1250e+06
Rg (reciprocal space) rg_reciprocal20.38
I(0) (reciprocal space) i0_reciprocal508200000.0000
Solution quality estimate total_estimate0.6864
Solution quality rating solution_quality REASONABLE a REASONABLE solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary20.3
Skewness Skewness skewness0.280
Kurtosis Kurtosis kurtosis-0.498
Angular range angular_range— – 0.3950 −1
Current regularization parameter α current_alpha2.9530
Highest regularization parameter α highest_alpha911700.0000
Real-space data points n_real_points71
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.004; Oscil: 0.993; Stabil: 0.982; Sysdev: 0.000; Positv: 1.000; Valcen: 0.998; Smooth: 0.000

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (1)

7. Fold Classification (SCOP + CATH) 3 domains

SCOP 2.08 (2 domains)

Domain ID domain_idd5xyla1
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.42 — POZ domain
Superfamily Superfamily superfamilyd.42.1 — POZ domain
Family Family familyd.42.1.0 — automated matches
Domain ID domain_idd5xyla2
Class classa — All alpha proteins
Fold Fold folda.157 — Skp1 dimerisation domain-like
Superfamily Superfamily superfamilya.157.1 — Skp1 dimerisation domain-like
Family Family familya.157.1.1 — Skp1 dimerisation domain-like

CATH v4.4 (1 domains)

Domain ID domain_id5xylA00
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology710 — Potassium Channel Kv1.1; Chain A
Homologous superfamily homologous superfamily10 — Potassium Channel Kv1.1; Chain A

8. Citations (1)

9. Files and Curves (10)