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

Structural Biology Knowledgebase: 4E9D SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.75 Å
  • R-Value Free: 0.330
  • R-Value Work: 0.267

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 4E9D

Classification: TRANSFERASE / TRANSFERASE INHIBITOR

Total Structure Weight: 27951.92

Macromolecule Entities
Molecule Chains Length Organism Details
Serine/threonine-protein kinase PLK1 A 232 Homo sapiens EC#: 2.7.11.21 IUBMB
Gene Name(s): PLK1 Gene View PLK
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
3-(1-benzothiophen-2-yl)propanoyl-derivatized DPPLHSpTA peptide E 10 synthetic

Small Molecules
Ligands 1 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
GOL
Query on GOL

A GLYCEROL
2, (Synonym)
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
Biologically Interesting Molecules 1 Unique
ID Chains Name Type/Class 2D Diagram 3D Interactions
PRD_000810 (SER,0OB,ALA,ASP,TPO,PRO,LEU,HIS,NH2) E 3-(1-benzothiophen-2-yl)propanoyl-derivatized DPPLHSpTA peptide Peptide-like /
Enzyme inhibitor
Ligand Explorer Electron Density (JSmol) Electron Density (JSmol) Electron Density (JSmol) Electron Density (JSmol) Electron Density (JSmol) Electron Density (JSmol) Electron Density (JSmol) Electron Density (JSmol) Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.75 Å
  • R-Value Free: 0.330
  • R-Value Work: 0.267
  • Space Group: P 1
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 35.87 α = 85.84
b = 36.30 β = 77.21
c = 47.47 γ = 68.24

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2012-03-21
  • Released Date: 2012-10-10
  • Deposition author(s): Sledz, P., Hyvonen, M., Lang, S., Stubbs, C.J., Abell, C.

Revision History

  • 2012-12-12
    Type: Other | Details: Add PRD info
  • 2012-10-17
    Type: Citation | Details: Citation update