6R6X | pdb_00006r6x

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 (Depositor), 0.251 (DCC)
R-Value Work:
0.199 (Depositor), 0.203 (DCC)
R-Value Observed:
0.201 (Depositor)

Starting Model: experimental
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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
Modeled Residue Count: 330
Deposited Residue Count: 337
Unique protein chains: 1

Macromolecules

Find similar proteins by:

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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% 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] mmCIF 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 (Depositor), 0.251 (DCC)
R-Value Work: 0.199 (Depositor), 0.203 (DCC)
R-Value Observed: 0.201 (Depositor)

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

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Ligand Structure Quality Assessment

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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

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), 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 R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.