6R6X

Crystal structure of di-phosphorylated human CLK1 in complex with 5-(1-methyl-1H-indol-3-yl)pyrimidin-4-amine

PDB DOI: https://doi.org/10.2210/pdb6R6X/pdb

Classification: SIGNALING PROTEIN
Organism(s): Homo sapiens
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2019-03-28 Released: 2020-05-06
Deposition Author(s): Livnah, O., Domovich, Y.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.05 Å
R-Value Free: 0.247
R-Value Work: 0.199
R-Value Observed: 0.201

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Crystal structure of di-phosphorylated human CLK1 in complex with 5-(1-methyl-1H-indol-3-yl)pyrimidin-4-amine

Livnah, O., Domovich, Y.

To be published.

Macromolecule Content

Total Structure Weight: 39.67 kDa
Atom Count: 2,853
Modelled Residue Count: 330
Deposited Residue Count: 337
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Dual specificity protein kinase CLK1	A	337	Homo sapiens	Mutation(s): 0 Gene Names: CLK1, CLK EC: 2.7.12.1
UniProt & NIH Common Fund Data Resources
Find proteins for P49759 (Homo sapiens) Explore P49759 Go to UniProtKB: P49759
PHAROS: P49759 GTEx: ENSG00000013441
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P49759
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
JU8 Query on JU8 Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A]	B [auth A]	5-(1-methylindol-3-yl)pyrimidin-4-amine C₁₃ H₁₂ N₄ IQUSYKXSEAUSFE-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.05 Å
R-Value Free: 0.247
R-Value Work: 0.199
R-Value Observed: 0.201
Space Group: P 6₅ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 68.24	α = 90
b = 68.24	β = 90
c = 283.54	γ = 120

Software Package:

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

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2020-05-06

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2020-05-06
Type: Initial release
Version 1.1: 2024-01-24
Changes: Data collection, Database references, Refinement description

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM133198.