1d9s

TUMOR SUPPRESSOR P15(INK4B) STRUCTURE BY COMPARATIVE MODELING AND NMR DATA

Method: SOLUTION NMR Dmax: 41.5 Å Quality: REASONABLE

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

CYCLIN-DEPENDENT KINASE 4 INHIBITOR B

Mus musculus

UniProt P55271

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 1–130 Not recorded No other associated polymer SOLUTION NMR NMR measurement conditions:pH 7.5;293 K;Ionic strength (raw mmCIF value) 0.1;Pressure AMBIENT NMR sample composition:0.2 MM P15, U-15N; 4 MM HEPES, 1 MM DTT, 5 UM EDTA | 95% H2O/5% D2O NMR sample composition:0.2 MM P15, U-15N,13C; 4 MM HEPES, 1 MM DTT, 5 UM EDTA | 95% H2O/5% D2O NMR sample composition:0.2 MM P15, U-15N,13C; 4 MM HEPES, 1 MM DTT, 5 UM EDTA | 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.

No other PDB entry for the same UniProt protein was found.

View Construct and Data Evidence
UniProt name CDN2B_MOUSE
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 1–136; UniProt 1–130

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 1d9s

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 1d9s
Download Download

2. Structure Basics 2. Structure Basics

Entry ID entry_id1d9s
Deposition date deposition_date1999-10-29
Structure title titleTUMOR SUPPRESSOR P15(INK4B) STRUCTURE BY COMPARATIVE MODELING AND NMR DATA
Keywords keywordsHELIX-TURN-HELIX, ANKYRIN REPEAT, SIGNALING PROTEIN; SIGNALING PROTEIN
Experimental Method methodSOLUTION NMR

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

Radius of gyration Rg (Guinier) rg_guinier15.94
Radius of gyration Rg (electron density) rg_electron15.62
Forward intensity I(0) i0333018000.00
Molecular weight molecular_weight143320.0 kDa
Excluded volume excluded_volume175780 ų
Envelope volume envelope_volume38984 ų
Hydration-shell volume shell_volume16958 ų
Envelope diameter envelope_diameter69.4
Shell Rg shell_rg26.41
Envelope Rg envelope_rg22.04
Shape Rg shape_rg15.62
Total Rg total_rg15.97
Total atoms total_atoms19950
Residues n_residues1360
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 dmax41.5
Rg (real space) rg_real14.70
Rg uncertainty (real space) rg_real_error0.06
I(0) (real space) i0_real3.1560e+08
I(0) uncertainty (real space) i0_real_error2.6100e+06
Rg (reciprocal space) rg_reciprocal16.11
I(0) (reciprocal space) i0_reciprocal333000000.0000
Solution quality estimate total_estimate0.6852
Solution quality rating solution_quality REASONABLE a REASONABLE solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary17.3
Skewness Skewness skewness0.285
Kurtosis Kurtosis kurtosis-0.368
Angular range angular_range— – 0.5000 −1
Current regularization parameter α current_alpha2.0280
Highest regularization parameter α highest_alpha610400.0000
Real-space data points n_real_points80
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.013; Oscil: 0.980; Stabil: 0.990; 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) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_idd1d9sa_
Class classi — Low resolution protein structures
Fold Fold foldi.11 — Computational models partly based on experimental data
Superfamily Superfamily superfamilyi.11.1 — Computational models partly based on experimental data
Family Family familyi.11.1.1 — Computational models partly based on experimental data

CATH v4.4 (1 domains)

Domain ID domain_id1d9sA00
Class class1 — Mainly Alpha
Architecture architecture25 — Alpha Horseshoe
Topology topology40 — Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat
Homologous superfamily homologous superfamily20 — Ankyrin repeat-containing domain

8. Citations (1)

9. Files and Curves (10)