6ax4

Plk-1 polo-box domain in complex with histidine N(tau)-cyclized Macrocycle 5b.

Method: X-RAY DIFFRACTION Dmax: 66.5 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 371–603 Fragment:UNP residues 367-603 histidine N(tau)-cyclized Macrocycle 5b × 1 AML AMYLAMINE × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;291 K;Well solution: 0.2 M Calcium Chloride, 12.5% PEG-3350 Protein: 10 mg/ml PBD-macrocycle complex in 0.5 M Sodium Chloride, 10 mM TRIS pH 8.0, 0.4 M ammonium acetate 1:1 mix of protein complex and well solution Resolution 1.45 Å R-free 0.166

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 6ax4

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 6ax4
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2. Structure Basics 2. Structure Basics

Entry ID entry_id6ax4
Deposition date deposition_date2017-09-06
Structure title titlePlk-1 polo-box domain in complex with histidine N(tau)-cyclized Macrocycle 5b.
Keywords keywordsmacrocyclic phosphopeptide, mitotic kinase. polo-box domain, PROTEIN BINDING; PROTEIN BINDING
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier19.30
Radius of gyration Rg (electron density) rg_electron18.19
Forward intensity I(0) i012417300.00
Molecular weight molecular_weight26523.0 kDa
Excluded volume excluded_volume33321 ų
Envelope volume envelope_volume38194 ų
Hydration-shell volume shell_volume17932 ų
Envelope diameter envelope_diameter69.4
Shell Rg shell_rg24.11
Envelope Rg envelope_rg18.43
Shape Rg shape_rg18.17
Total Rg total_rg19.15
Total atoms total_atoms3727
Residues n_residues223
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 dmax66.5
Rg (real space) rg_real19.29
Rg uncertainty (real space) rg_real_error0.47
I(0) (real space) i0_real1.2420e+07
I(0) uncertainty (real space) i0_real_error1.7420e+05
Rg (reciprocal space) rg_reciprocal19.29
I(0) (reciprocal space) i0_reciprocal12420000.0000
Solution quality estimate total_estimate0.7812
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks3
Primary peak position r_peak_primary23.4
Skewness Skewness skewness0.399
Kurtosis Kurtosis kurtosis-0.080
Angular range angular_range— – 0.4100 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha3732000.0000
Real-space data points n_real_points72
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.727; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.971; Smooth: 0.000

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_id6ax4A01
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_id6ax4A02
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)