5nn1

The structure of the polo-box domain (PBD) of polo-like kinase 1 (Plk1)

Method: X-RAY DIFFRACTION Dmax: 67.9 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 monomer Monomer Protein × 1 PDB declaration: monomeric(1) Consistent with protein copy count Chain A; UniProt 371–603 Fragment:Polo-box domain, UNP residues 371-603 No other associated polymer X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION;298 K;200 mM Na/K Tartrate, 10-20% PEG3350 Resolution 1.78 Å R-free 0.245

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 5–237; UniProt 371–603

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 5nn1

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 5nn1
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2. Structure Basics 2. Structure Basics

Entry ID entry_id5nn1
Deposition date deposition_date2017-04-07
Structure title titleThe structure of the polo-box domain (PBD) of polo-like kinase 1 (Plk1)
Keywords keywordsPLK1, PBD1, mitosis, transferase; TRANSFERASE
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_electron18.14
Forward intensity I(0) i010840900.00
Molecular weight molecular_weight24519.0 kDa
Excluded volume excluded_volume30690 ų
Envelope volume envelope_volume35283 ų
Hydration-shell volume shell_volume16842 ų
Envelope diameter envelope_diameter71.7
Shell Rg shell_rg23.78
Envelope Rg envelope_rg18.47
Shape Rg shape_rg18.12
Total Rg total_rg19.06
Total atoms total_atoms1723
Residues n_residues215
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 dmax67.9
Rg (real space) rg_real19.26
Rg uncertainty (real space) rg_real_error0.57
I(0) (real space) i0_real1.0840e+07
I(0) uncertainty (real space) i0_real_error1.4180e+05
Rg (reciprocal space) rg_reciprocal19.26
I(0) (reciprocal space) i0_reciprocal10840000.0000
Solution quality estimate total_estimate0.7643
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks3
Primary peak position r_peak_primary22.6
Skewness Skewness skewness0.436
Kurtosis Kurtosis kurtosis-0.056
Angular range angular_range— – 0.4150 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha2596000.0000
Real-space data points n_real_points73
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.661; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.952; Smooth: 0.000

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (2)

7. Fold Classification (SCOP + CATH) 5 domains

SCOP 2.08 (3 domains)

Domain ID domain_idd5nn1a1
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.223 — Polo-box domain
Superfamily Superfamily superfamilyd.223.1 — Polo-box domain
Family Family familyd.223.1.2 — Polo-box duplicated region
Domain ID domain_idd5nn1a2
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.223 — Polo-box domain
Superfamily Superfamily superfamilyd.223.1 — Polo-box domain
Family Family familyd.223.1.2 — Polo-box duplicated region
Domain ID domain_idd5nn1a3
Class classl — Artifacts
Fold Fold foldl.1 — Tags
Superfamily Superfamily superfamilyl.1.1 — Tags
Family Family familyl.1.1.1 — Tags

CATH v4.4 (2 domains)

Domain ID domain_id5nn1A01
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_id5nn1A02
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)