4E67 | pdb_00004e67

The structure of the polo-box domain (PBD) of polo-like kinase 1 (Plk1) in complex with hydrocinnamoyl-derivatized PLHSpTA peptide

PDB DOI: https://doi.org/10.2210/pdb4E67/pdb

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

Deposited: 2012-03-15 Released: 2012-10-10
Deposition Author(s): Sledz, P., Hyvonen, M., Tan, Y.S., Lang, S., Spring, D., Abell, C., Best, R.B.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free:
0.265 (Depositor), 0.266 (DCC)
R-Value Work:
0.216 (Depositor), 0.216 (DCC)
R-Value Observed:
0.218 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 1.3 of the entry. See complete history.

Literature

Using ligand-mapping simulations to design a ligand selectively targeting a cryptic surface pocket of polo-like kinase 1.

Tan, Y.S., Sledz, P., Lang, S., Stubbs, C.J., Spring, D.R., Abell, C., Best, R.B.

(2012) Angew Chem Int Ed Engl 51: 10078-10081

PubMed: 22961729 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1002/anie.201205676
Primary Citation Related Structures:
4E67

Organizational Affiliation

Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW UK.

Macromolecule Content

Total Structure Weight: 27.59 kDa
Atom Count: 1,851
Modeled Residue Count: 221
Deposited Residue Count: 240
Unique protein chains: 2

Macromolecules

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| 3D Structure

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 Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P53350
Sequence Annotations Expand
Reference Sequence

Find similar proteins by: Sequence | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
hydrocinnamoyl-derivatized PLHSpTA peptide	B	8	N/A	Mutation(s): 0

Small Molecules

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
TPO Query on 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_000807 Query on PRD_000807	B	hydrocinnamoyl-derivatized PLHSpTA peptide	Peptide-like / Enzyme inhibitor		Interactions Focus chain B Interactions & Density Focus chain B

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free: 0.265 (Depositor), 0.266 (DCC)
R-Value Work: 0.216 (Depositor), 0.216 (DCC)
R-Value Observed: 0.218 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 35.492	α = 90
b = 50.906	β = 101.01
c = 57.91	γ = 90

Software Package:

Software Name	Purpose
PROTEUM PLUS	data collection
PHASER	phasing
REFMAC	refinement
PROTEUM PLUS	data reduction
PROTEUM PLUS	data scaling

Structure Validation

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Entry History

Deposition Data

Released Date: 2012-10-10

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2012-10-10
Type: Initial release
Version 1.1: 2012-12-12
Changes: Other
Version 1.2: 2023-09-13
Changes: Data collection, Database references, Derived calculations, Refinement description
Version 1.3: 2024-11-27
Changes: Structure summary