4E9C | pdb_00004e9c

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

• PDB DOI: https://doi.org/10.2210/pdb4E9C/pdb

• Classification: TRANSFERASE/TRANSFERASE INHIBITOR
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


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

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 
  0.232 (Depositor), 0.232 (DCC) 
• R-Value Work: 
  0.192 (Depositor) 
• R-Value Observed: 
  0.194 (Depositor) 

Starting Model: experimental

Literature

High-throughput interrogation of ligand binding mode using a fluorescence-based assay.

Sledz, P., Lang, S., Stubbs, C.J., Abell, C.

(2012) Angew Chem Int Ed Engl 51: 7680-7683

• PubMed: 22730171 
• DOI: https://doi.org/10.1002/anie.201202660
• Primary Citation Related Structures: 
  4E9C, 4E9D


• PubMed Abstract: 
  

  Probing the pocket: A high-throughput fluorescence-based thermal shift (FTS) assay utilized different forms of a protein (in gray) to establish the binding mode of a ligand (see picture). The assay serves in the rapid evaluation of structure-activity binding-mode relationships for a series of ligands of Plk1, an important target of anticancer therapy.

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Organizational Affiliation: 
• University Chemical Laboratory, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 28.14 kDa 
• Atom Count: 2,076 
• Modeled Residue Count: 231 
• Deposited Residue Count: 243 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Serine/threonine-protein kinase PLK1	A	232	Homo sapiens	Mutation(s): 0  Gene Names: PLK1, PLK EC: 2.7.11.21
UniProt & NIH Common Fund Data Resources
Find proteins for P53350 (Homo sapiens) Explore P53350  Go to UniProtKB:  P53350
PHAROS:  P53350 GTEx:  ENSG00000166851

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
LDPPLHSpTA phosphopeptide	B	11	N/A	Mutation(s): 0

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PG0	C [auth A], D [auth A]	2-(2-METHOXYETHOXY)ETHANOL C5 H12 O3 SBASXUCJHJRPEV-UHFFFAOYSA-N
GOL	E [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
TPO	B	L-PEPTIDE LINKING	C4 H10 N O6 P		THR

Biologically Interesting Molecules (External Reference) 

1 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_000809	B	LDPPLHSpTA phosphopeptide	Peptide-like / Enzyme inhibitor

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free:  0.232 (Depositor), 0.232 (DCC) 
• R-Value Work:  0.192 (Depositor) 
• R-Value Observed: 0.194 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 35.634	α = 90
b = 89.784	β = 109.28
c = 37.108	γ = 90

Software Package:

Software Name	Purpose
MOLREP	phasing
REFMAC	refinement
XDS	data reduction
XDS	data scaling

Structure Validation

Entry History 

Deposition Data

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

Revision History  

• Version 1.0: 2012-10-10
  Type: Initial release
  
• Version 1.1: 2012-10-17
  Changes: Database references
• Version 1.2: 2012-12-12
  Changes: Other
• Version 1.3: 2018-12-05
  Changes: Data collection, Database references
• Version 1.4: 2023-09-13
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.5: 2024-11-06
  Changes: Structure summary