4E9C

The structure of the polo-box domain (PBD) of polo-like kinase 1 (Plk1) in complex with LDPPLHSpTA phosphopeptide

Structural Biology Knowledgebase: 4E9C SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.232
  • R-Value Work: 0.192

Literature

Macromolecules
Sequence Display for 4E9C

Classification: TRANSFERASE / TRANSFERASE INHIBITOR

Total Structure Weight: 28143.16

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
LDPPLHSpTA phosphopeptide B 11 synthetic

Small Molecules
Ligands 2 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
PG0
Query on PG0

A 2-(2-METHOXYETHOXY)ETHANOL
PEG 6000 (Synonym)
C5 H12 O3
SBASXUCJHJRPEV-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
GOL
Query on GOL

B GLYCEROL
2, (Synonym)
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
Biologically Interesting Molecules 1 Unique
ID Chains Name Type/Class 2D Diagram 3D Interactions
PRD_000809
Query on PRD_000809
B LDPPLHSpTA phosphopeptide 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)
Modified Residues 3 Unique
ID Chains Type Formula 2D Diagram Parent
ACE
Query on ACE
B NON-POLYMER C2 H4 O --
TPO
Query on TPO
B L-PEPTIDE LINKING C4 H10 N O6 P THR
NH2
Query on NH2
B NON-POLYMER H2 N --

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.232
  • R-Value Work: 0.192
  • Space Group: P 1 21 1
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 35.63 α = 90.00
b = 89.78 β = 109.28
c = 37.11 γ = 90.00

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