4hab

Crystal structure of Plk1 Polo-box domain in complex with PL-49

Method: X-RAY DIFFRACTION Dmax: 111.3 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 371–593 Not recorded PL-49 × 1 CXS 3-CYCLOHEXYL-1-PROPYLSULFONIC ACID × 2 PO4 PHOSPHATE ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION;pH 10;293 K;0.1M CAPS pH 8, 0.2M LiSO4, 0.8M K2HPO4 NaH2PO4, vapor diffusion, temperature 293K Resolution 2.65 Å R-free 0.259
2 Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain B; UniProt 371–593 Not recorded PL-49 × 1 CXS 3-CYCLOHEXYL-1-PROPYLSULFONIC ACID × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION;pH 10;293 K;0.1M CAPS pH 8, 0.2M LiSO4, 0.8M K2HPO4 NaH2PO4, vapor diffusion, temperature 293K Resolution 2.65 Å R-free 0.259
3 Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain C; UniProt 371–593 Not recorded PL-49 × 1 CXS 3-CYCLOHEXYL-1-PROPYLSULFONIC ACID × 2 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION;pH 10;293 K;0.1M CAPS pH 8, 0.2M LiSO4, 0.8M K2HPO4 NaH2PO4, vapor diffusion, temperature 293K Resolution 2.65 Å R-free 0.259

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 110 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 1–223; UniProt 371–593 Author chain B; PDBConstruct 1–223; UniProt 371–593 Author chain C; PDBConstruct 1–223; UniProt 371–593

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 4hab

P(r) Distance Distribution P(r) Distribution

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

Entry ID entry_id4hab
Deposition date deposition_date2012-09-26
Structure title titleCrystal structure of Plk1 Polo-box domain in complex with PL-49
Keywords keywordsPolo-box domain, 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_guinier33.50
Radius of gyration Rg (electron density) rg_electron33.26
Forward intensity I(0) i091545500.00
Molecular weight molecular_weight76595.0 kDa
Excluded volume excluded_volume96056 ų
Envelope volume envelope_volume125310 ų
Hydration-shell volume shell_volume33041 ų
Envelope diameter envelope_diameter116.5
Shell Rg shell_rg38.14
Envelope Rg envelope_rg32.98
Shape Rg shape_rg33.26
Total Rg total_rg33.64
Total atoms total_atoms5372
Residues n_residues640
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 dmax111.3
Rg (real space) rg_real33.68
Rg uncertainty (real space) rg_real_error1.00
I(0) (real space) i0_real9.1550e+07
I(0) uncertainty (real space) i0_real_error1.6740e+06
Rg (reciprocal space) rg_reciprocal33.57
I(0) (reciprocal space) i0_reciprocal91540000.0000
Solution quality estimate total_estimate0.8548
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary30.8
Skewness Skewness skewness0.442
Kurtosis Kurtosis kurtosis-0.491
Angular range angular_range— – 0.2350 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha33860000.0000
Real-space data points n_real_points48
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.848; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.765; Smooth: 0.800

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (5)

7. Fold Classification (SCOP + CATH) 6 domains

CATH v4.4 (6 domains)

Domain ID domain_id4habA01
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_id4habA02
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_id4habB01
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_id4habB02
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_id4habC01
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_id4habC02
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)