6KYQ | pdb_00006kyq

Crystal structure of DCLK1 Autoinhibited Kinase Domain

PDB DOI: https://doi.org/10.2210/pdb6KYQ/pdb

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

Deposited: 2019-09-20 Released: 2020-09-23
Deposition Author(s): Yu, Y., Chen, Q.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.14 Å
R-Value Free:
0.198 (Depositor), 0.201 (DCC)
R-Value Work:
0.161 (Depositor), 0.162 (DCC)
R-Value Observed:
0.169 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Validation slider image for 6KYQ

This is version 1.2 of the entry. See complete history.

Literature

DCLK1 Autoinhibition and Activation in Tumorigenesis

Cheng, L., Yang, Z., Guo, W., Wu, C., Liang, S., Tong, A., Cao, Z., Thorne, R.F., Yang, S.Y., Yu, Y., Chen, Q.

(2021) Innovation (Camb)

DOI: https://doi.org/10.1016/j.xinn.2021.100191

Macromolecule Content

Total Structure Weight: 73.39 kDa
Atom Count: 5,429
Modeled Residue Count: 635
Deposited Residue Count: 656
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Serine/threonine-protein kinase DCLK1	A, B	328	Homo sapiens	Mutation(s): 0 Gene Names: DCLK1, DCAMKL1, DCDC3A, KIAA0369 EC: 2.7.11.1
UniProt & NIH Common Fund Data Resources
Find proteins for O15075 (Homo sapiens) Explore O15075 Go to UniProtKB: O15075
PHAROS: O15075 GTEx: ENSG00000133083
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	O15075
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
BME Query on BME Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [auth B] mmCIF format, chain C [auth A] mmCIF format, chain D [auth B]	C [auth A], D [auth B]	BETA-MERCAPTOETHANOL C₂ H₆ O S DGVVWUTYPXICAM-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.14 Å
R-Value Free: 0.198 (Depositor), 0.201 (DCC)
R-Value Work: 0.161 (Depositor), 0.162 (DCC)
R-Value Observed: 0.169 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 77.6	α = 90
b = 77.522	β = 90
c = 178.119	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PDB_EXTRACT	data extraction
HKL-3000	data reduction
HKL-3000	data scaling
PHASER	phasing

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2020-09-23

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2020-09-23
Type: Initial release
Version 1.1: 2021-12-08
Changes: Database references
Version 1.2: 2023-11-22
Changes: Data collection, Database references, Refinement description

RCSB PDB is hosted by

RCSB PDB is a member of

RCSB Partners
Nucleic Acid Knowledgebase

CoreTrustSeal

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.