4e9c

The structure of the polo-box domain (PBD) of polo-like kinase 1 (Plk1) in complex with LDPPLHSpTA phosphopeptide

Method: X-RAY DIFFRACTION Dmax: 74.8 Å Quality: REASONABLE

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 371–594 Not recorded LDPPLHSpTA phosphopeptide × 1 PG0 2-(2-METHOXYETHOXY)ETHANOL × 2 GOL GLYCEROL × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 6.5;293 K;0.1 M MES pH 6.5, 30% PEG 300, VAPOR DIFFUSION, SITTING DROP, temperature 293K Resolution 1.70 Å R-free 0.232

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 112 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 9–232; UniProt 371–594

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 4e9c

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 4e9c
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2. Structure Basics 2. Structure Basics

Entry ID entry_id4e9c
Deposition date deposition_date2012-03-21
Structure title titleThe structure of the polo-box domain (PBD) of polo-like kinase 1 (Plk1) in complex with LDPPLHSpTA phosphopeptide
Keywords keywordsserine/threonine kinase, transferase, phosphoprotein binding domain, TRANSFERASE-TRANSFERASE INHIBITOR complex; TRANSFERASE/TRANSFERASE INHIBITOR
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier19.24
Radius of gyration Rg (electron density) rg_electron18.15
Forward intensity I(0) i012649300.00
Molecular weight molecular_weight26559.0 kDa
Excluded volume excluded_volume33266 ų
Envelope volume envelope_volume38323 ų
Hydration-shell volume shell_volume17988 ų
Envelope diameter envelope_diameter71.3
Shell Rg shell_rg24.25
Envelope Rg envelope_rg18.45
Shape Rg shape_rg18.14
Total Rg total_rg19.11
Total atoms total_atoms1866
Residues n_residues229
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 dmax74.8
Rg (real space) rg_real19.21
Rg uncertainty (real space) rg_real_error0.62
I(0) (real space) i0_real1.2650e+07
I(0) uncertainty (real space) i0_real_error1.4790e+05
Rg (reciprocal space) rg_reciprocal19.21
I(0) (reciprocal space) i0_reciprocal12650000.0000
Solution quality estimate total_estimate0.7115
Solution quality rating solution_quality REASONABLE a REASONABLE solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary22.9
Skewness Skewness skewness0.392
Kurtosis Kurtosis kurtosis-0.041
Angular range angular_range— – 0.4150 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha3808000.0000
Real-space data points n_real_points73
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.471; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.832; Smooth: 0.000

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (5)

7. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id4e9cA01
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_id4e9cA02
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)