3NR9

Structure of human CDC2-like kinase 2 (CLK2)

PDB DOI: https://doi.org/10.2210/pdb3NR9/pdb

Classification: TRANSFERASE
Organism(s): Homo sapiens
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2010-06-30 Released: 2010-08-25
Deposition Author(s): Chaikuad, A., Savitsky, P., Krojer, T., Muniz, J.R.C., Filippakopoulos, P., Rellos, P., Keates, T., Fedorov, O., Pike, A.C.W., Eswaran, J., Berridge, G., Phillips, C., Zhang, Y., von Delft, F., Weigelt, J., Arrowsmith, C.H., Edwards, A.M., Bountra, C., Knapp, S., Structural Genomics Consortium (SGC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.89 Å
R-Value Free: 0.252
R-Value Work: 0.194
R-Value Observed: 0.197

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Structure of human CDC2-like kinase 2 (CLK2)

Chaikuad, A., Savitsky, P., Krojer, T., Muniz, J.R.C., Filippakopoulos, P., Rellos, P., Keates, T., Fedorov, O., Pike, A.C.W., Eswaran, J., Berridge, G., Phillips, C., Zhang, Y., von Delft, F., Weigelt, J., Arrowsmith, C.H., Edwards, A.M., Bountra, C., Knapp, S., Structural Genomics Consortium (SGC)

To be published.

Macromolecule Content

Total Structure Weight: 131.22 kDa
Atom Count: 8,562
Modelled Residue Count: 1,035
Deposited Residue Count: 1,104
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Dual specificity protein kinase CLK2	A, B, C	368	Homo sapiens	Mutation(s): 0 Gene Names: CLK2 EC: 2.7.12.1
UniProt & NIH Common Fund Data Resources
Find proteins for P49760 (Homo sapiens) Explore P49760 Go to UniProtKB: P49760
PHAROS: P49760 GTEx: ENSG00000176444
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P49760
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NR9 Query on NR9 Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain E [auth B] SDF format, chain F [auth C] MOL2 format, chain D [auth A] MOL2 format, chain E [auth B] MOL2 format, chain F [auth C] mmCIF format, chain D [auth A] mmCIF format, chain E [auth B] mmCIF format, chain F [auth C]	D [auth A], E [auth B], F [auth C]	(5Z)-5-(quinolin-6-ylmethylidene)-2-[(thiophen-2-ylmethyl)amino]-1,3-thiazol-4(5H)-one C₁₈ H₁₃ N₃ O S₂ XOLMRFUGOINFDQ-YBEGLDIGSA-N		Interactions Focus chain D [auth A] Focus chain E [auth B] Focus chain F [auth C] Interactions & Density Focus chain D [auth A] Focus chain E [auth B] Focus chain F [auth C]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.89 Å
R-Value Free: 0.252
R-Value Work: 0.194
R-Value Observed: 0.197
Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 97.678	α = 90
b = 97.678	β = 90
c = 223.029	γ = 120

Software Package:

Software Name	Purpose
PHASER	phasing
REFMAC	refinement
XDS	data reduction
SCALA	data scaling

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2010-08-25

Deposition Author(s):

Structural Genomics Consortium (SGC)

Revision History (Full details and data files)

Version 1.0: 2010-08-25
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2017-11-08
Changes: Refinement description
Version 1.3: 2023-09-06
Changes: Data collection, Database references, Derived calculations, Refinement description

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Help and Resources

3NR9

Structure of human CDC2-like kinase 2 (CLK2)

Structure of human CDC2-like kinase 2 (CLK2)

Entity ID: 1

UniProt & NIH Common Fund Data Resources

Entity Groups

Sequence Annotations

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Experimental Data

Structure Validation

Ligand Structure Quality Assessment

Deposition Data

Revision History (Full details and data files)