4e9d

The structure of the polo-box domain (PBD) of polo-like kinase 1 (Plk1) in complex with 3-(1-benzothiophen-2-yl)propanoyl-derivatized DPPLHSpTA peptide

Method: X-RAY DIFFRACTION Dmax: 70.6 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 371–594 Not recorded 3-(1-benzothiophen-2-yl)propanoyl-derivatized DPPLHSpTA peptide × 1 GOL GLYCEROL × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;293 K;0.1 M sodium acetate, 1.0 M LiCl, 30% PEG 6000, VAPOR DIFFUSION, SITTING DROP, temperature 293K Resolution 2.75 Å R-free 0.330

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 4e9d

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 4e9d
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2. Structure Basics 2. Structure Basics

Entry ID entry_id4e9d
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 3-(1-benzothiophen-2-yl)propanoyl-derivatized DPPLHSpTA peptide
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_guinier19.17
Radius of gyration Rg (electron density) rg_electron18.38
Forward intensity I(0) i022769800.00
Molecular weight molecular_weight24336.0 kDa
Excluded volume excluded_volume23538 ų
Envelope volume envelope_volume38858 ų
Hydration-shell volume shell_volume18122 ų
Envelope diameter envelope_diameter68.3
Shell Rg shell_rg24.26
Envelope Rg envelope_rg18.53
Shape Rg shape_rg18.34
Total Rg total_rg19.10
Total atoms total_atoms1839
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 dmax70.6
Rg (real space) rg_real19.15
Rg uncertainty (real space) rg_real_error0.52
I(0) (real space) i0_real2.2770e+07
I(0) uncertainty (real space) i0_real_error3.1210e+05
Rg (reciprocal space) rg_reciprocal19.16
I(0) (reciprocal space) i0_reciprocal22770000.0000
Solution quality estimate total_estimate0.8240
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary22.6
Skewness Skewness skewness0.407
Kurtosis Kurtosis kurtosis-0.078
Angular range angular_range— – 0.4150 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha6540000.0000
Real-space data points n_real_points73
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.601; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.908; Smooth: 0.997

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (4)

7. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id4e9dA01
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_id4e9dA02
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)