5j19

phospho-Pon binding-induced Plk1 dimerization

Method: X-RAY DIFFRACTION Dmax: 85.3 Å Quality: GOOD

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

Serine/threonine-protein kinase PLK1

Homo sapiens

UniProt P53350

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 367–594 Fragment:Polo-box domain, UNP residues 367-594 Phosphorylated peptide from Partner of Numb × 1 (O96561) GOL GLYCEROL × 1 X-RAY DIFFRACTION X-ray crystallization conditions:EVAPORATION;pH 5.5;289 K;PEG 3350, NaCOOH Resolution 2.00 Å R-free 0.236
2 Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain B; UniProt 367–594 Fragment:Polo-box domain, UNP residues 367-594 Phosphorylated peptide from Partner of Numb × 1 (O96561) GOL GLYCEROL × 2 X-RAY DIFFRACTION X-ray crystallization conditions:EVAPORATION;pH 5.5;289 K;PEG 3350, NaCOOH Resolution 2.00 Å R-free 0.236

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.

84 other PDB entries and 111 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name PLK1_HUMAN
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 7–234; UniProt 367–594 Author chain B; PDBConstruct 7–234; UniProt 367–594

Phosphorylated peptide from Partner of Numb

OrganismNot specified

UniProt O96561

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 D; UniProt 52–66 Non-standard monomer:Yes (specific site not provided by mmCIF) Serine/threonine-protein kinase PLK1 × 1 (P53350) GOL GLYCEROL × 1 X-RAY DIFFRACTION X-ray crystallization conditions:EVAPORATION;pH 5.5;289 K;PEG 3350, NaCOOH Resolution 2.00 Å R-free 0.236
2 Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain C; UniProt 52–66 Non-standard monomer:Yes (specific site not provided by mmCIF) Serine/threonine-protein kinase PLK1 × 1 (P53350) GOL GLYCEROL × 2 X-RAY DIFFRACTION X-ray crystallization conditions:EVAPORATION;pH 5.5;289 K;PEG 3350, NaCOOH Resolution 2.00 Å R-free 0.236

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 O96561_DROME
Isoform
PDB entities 2
Chains and sequence ranges Author chain C; PDBConstruct 1–15; UniProt 52–66 Author chain D; PDBConstruct 1–15; UniProt 52–66

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 5j19

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 5j19
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2. Structure Basics 2. Structure Basics

Entry ID entry_id5j19
Deposition date deposition_date2016-03-29
Structure title titlephospho-Pon binding-induced Plk1 dimerization
Keywords keywordsPolo-box domain, CELL CYCLE; CELL CYCLE
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier26.45
Radius of gyration Rg (electron density) rg_electron25.56
Forward intensity I(0) i043222600.00
Molecular weight molecular_weight50974.0 kDa
Excluded volume excluded_volume63751 ų
Envelope volume envelope_volume77412 ų
Hydration-shell volume shell_volume26014 ų
Envelope diameter envelope_diameter89.4
Shell Rg shell_rg31.99
Envelope Rg envelope_rg25.63
Shape Rg shape_rg25.56
Total Rg total_rg26.28
Total atoms total_atoms3591
Residues n_residues466
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 dmax85.3
Rg (real space) rg_real26.54
Rg uncertainty (real space) rg_real_error0.59
I(0) (real space) i0_real4.3220e+07
I(0) uncertainty (real space) i0_real_error6.0350e+05
Rg (reciprocal space) rg_reciprocal26.51
I(0) (reciprocal space) i0_reciprocal43220000.0000
Solution quality estimate total_estimate0.8848
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary25.6
Skewness Skewness skewness0.419
Kurtosis Kurtosis kurtosis-0.432
Angular range angular_range— – 0.3000 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha14700000.0000
Real-space data points n_real_points61
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.879; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.939; Smooth: 0.922

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (4)

7. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

Domain ID domain_id5j19A01
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology1120 — Arylsulfatase, C-terminal domain
Homologous superfamily homologous superfamily30 — POLO box domain
Domain ID domain_id5j19A02
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology1120 — Arylsulfatase, C-terminal domain
Homologous superfamily homologous superfamily30 — POLO box domain
Domain ID domain_id5j19B01
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology1120 — Arylsulfatase, C-terminal domain
Homologous superfamily homologous superfamily30 — POLO box domain
Domain ID domain_id5j19B02
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology1120 — Arylsulfatase, C-terminal domain
Homologous superfamily homologous superfamily30 — POLO box domain

8. Citations (1)

9. Files and Curves (10)