1q4o

The structure of the polo box domain of human Plk1

Method: X-RAY DIFFRACTION Dmax: 103.6 Å Quality: REASONABLE

1. Protein Identity and Related Structures Protein Identity & Related Structures

Serine/threonine-protein kinase PLK

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 367–603 Fragment:Polo box domain of Plk1 No other associated polymer X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 6;293 K;PEG 4000, sodium citrate and ammonium acetate, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K Resolution 2.20 Å R-free 0.288
2 Protein monomer Monomer Protein × 1 PDB declaration: monomeric(1) Consistent with protein copy count Chain B; UniProt 367–603 Fragment:Polo box domain of Plk1 No other associated polymer X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 6;293 K;PEG 4000, sodium citrate and ammonium acetate, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K Resolution 2.20 Å R-free 0.288

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 111 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 1–237; UniProt 367–603 Author chain B; PDBConstruct 1–237; UniProt 367–603

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 1q4o

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 1q4o
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2. Structure Basics 2. Structure Basics

Entry ID entry_id1q4o
Deposition date deposition_date2003-08-04
Structure title titleThe structure of the polo box domain of human Plk1
Keywords keywordsTransferase, Serine/threonine-protein kinase, ATP-binding, Nuclear protein; TRANSFERASE
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier30.92
Radius of gyration Rg (electron density) rg_electron30.82
Forward intensity I(0) i037058900.00
Molecular weight molecular_weight48294.0 kDa
Excluded volume excluded_volume60608 ų
Envelope volume envelope_volume76286 ų
Hydration-shell volume shell_volume22488 ų
Envelope diameter envelope_diameter108.8
Shell Rg shell_rg34.72
Envelope Rg envelope_rg30.76
Shape Rg shape_rg30.81
Total Rg total_rg31.19
Total atoms total_atoms3395
Residues n_residues415
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 dmax103.6
Rg (real space) rg_real31.34
Rg uncertainty (real space) rg_real_error1.08
I(0) (real space) i0_real3.7060e+07
I(0) uncertainty (real space) i0_real_error6.0040e+05
Rg (reciprocal space) rg_reciprocal31.16
I(0) (reciprocal space) i0_reciprocal37050000.0000
Solution quality estimate total_estimate0.5351
Solution quality rating solution_quality REASONABLE a REASONABLE solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary22.4
Skewness Skewness skewness0.511
Kurtosis Kurtosis kurtosis-0.588
Angular range angular_range— – 0.2550 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha14250000.0000
Real-space data points n_real_points52
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.569; Stabil: 0.999; Sysdev: 0.115; Positv: 1.000; Valcen: 0.322; Smooth: 0.581

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (2)

7. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

Domain ID domain_idd1q4oa1
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_idd1q4oa2
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_idd1q4ob1
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_idd1q4ob2
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

CATH v4.4 (4 domains)

Domain ID domain_id1q4oA01
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_id1q4oA02
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_id1q4oB01
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_id1q4oB02
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)