4O56

Structure of PLK1 in complex with peptide

PDB DOI: https://doi.org/10.2210/pdb4O56/pdb

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

Deposited: 2013-12-19 Released: 2014-12-24
Deposition Author(s): Wang, T.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free: 0.201
R-Value Work: 0.140
R-Value Observed: 0.143

wwPDB Validation 3D Report Full Report

This is version 1.1 of the entry. See complete history.

Literature

Integration of Charge-dipole Interaction and Intramolecular Hydrogen Bond in Ligand Design for the Polo-Box Domain of Polo-like Kinase 1

Quan, J.M., Wang, T., Shan, H.M.

To be published.

Macromolecule Content

Total Structure Weight: 29.11 kDa
Atom Count: 2,287
Modelled Residue Count: 252
Deposited Residue Count: 252
Unique protein chains: 2

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Serine/threonine-protein kinase PLK1	A	244	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% Identity50% Identity70% Identity90% Identity95% Identity100% 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
synthetic peptide	B	8	N/A	Mutation(s): 0
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PO4 Query on PO4 Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth A] SDF format, chain E [auth A] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A]	C [auth A], D [auth A], E [auth A]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A]

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

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free: 0.201
R-Value Work: 0.140
R-Value Observed: 0.143
Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 35.114	α = 90
b = 69.248	β = 98.63
c = 56.513	γ = 90

Software Package:

Software Name	Purpose
CrystalClear	data collection
PHASER	phasing
REFMAC	refinement
CrystalClear	data reduction
CrystalClear	data scaling

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2014-12-24

Deposition Author(s):

Wang, T.

Revision History (Full details and data files)

Version 1.0: 2014-12-24
Type: Initial release
Version 1.1: 2023-11-08
Changes: Data collection, Database references, Derived calculations, Refinement description

Prepare Data

Validate Data

Deposit Data

Help and Resources

4O56

Structure of PLK1 in complex with peptide

Integration of Charge-dipole Interaction and Intramolecular Hydrogen Bond in Ligand Design for the Polo-Box Domain of Polo-like Kinase 1

Entity ID: 1

UniProt & NIH Common Fund Data Resources

Entity Groups

Sequence Annotations

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