6GRO | pdb_00006gro

Human CSNK1G3 bound to SB-223133

PDB DOI: https://doi.org/10.2210/pdb6GRO/pdb

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

Deposited: 2018-06-12 Released: 2018-06-20
Deposition Author(s): Szklarz, M., Vollmar, M., von Delft, F., Bountra, C., Knapp, S., Edwards, A.M., Arrowsmith, C., Elkins, J.M.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.45 Å
R-Value Free:
0.167 (Depositor), 0.170 (DCC)
R-Value Work:
0.134 (Depositor), 0.140 (DCC)
R-Value Observed:
0.135 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

CSNK1G3 bound to SB-223133

Szklarz, M., Elkins, J.M.

To be published.

Macromolecule Content

Total Structure Weight: 39.19 kDa
Atom Count: 2,846
Modeled Residue Count: 293
Deposited Residue Count: 330
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Casein kinase I isoform gamma-3	A	330	Homo sapiens	Mutation(s): 0 Gene Names: CSNK1G3 EC: 2.7.11.1
UniProt & NIH Common Fund Data Resources
Find proteins for Q9Y6M4 (Homo sapiens) Explore Q9Y6M4 Go to UniProtKB: Q9Y6M4
PHAROS: Q9Y6M4 GTEx: ENSG00000151292
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9Y6M4
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
F92 Query on F92 Download Ideal Coordinates CCD File SDF format, chain G [auth A] MOL2 format, chain G [auth A] mmCIF format, chain G [auth A]	G [auth A]	4-[5-(2-azanylpyrimidin-4-yl)-4-(4-fluorophenyl)imidazol-1-yl]cyclohexan-1-ol C₁₉ H₂₀ F N₅ O YNEJNUAUXPCFAS-SHTZXODSSA-N		Interactions Focus chain G [auth A] Interactions & Density Focus chain G [auth A]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain B [auth A] SDF format, chain C [auth A] SDF format, chain E [auth A] SDF format, chain F [auth A] MOL2 format, chain B [auth A] MOL2 format, chain C [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] mmCIF format, chain B [auth A] mmCIF format, chain C [auth A] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A]	B [auth A], C [auth A], E [auth A], F [auth A]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Focus chain C [auth A] Focus chain E [auth A] Focus chain F [auth A] Interactions & Density Focus chain B [auth A] Focus chain C [auth A] Focus chain E [auth A] Focus chain F [auth A]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain D [auth A] MOL2 format, chain D [auth A] mmCIF format, chain D [auth A]	D [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.45 Å
R-Value Free: 0.167 (Depositor), 0.170 (DCC)
R-Value Work: 0.134 (Depositor), 0.140 (DCC)
R-Value Observed: 0.135 (Depositor)

Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 56.75	α = 90
b = 56.75	β = 90
c = 221.55	γ = 120

Software Package:

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

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2018-06-20

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2018-06-20
Type: Initial release
Version 1.1: 2019-02-20
Changes: Data collection, Derived calculations
Version 1.2: 2019-07-10
Changes: Data collection
Version 1.3: 2024-01-17
Changes: Data collection, Database references, Refinement description

Prepare Data

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Deposit Data

Help and Resources

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Human CSNK1G3 bound to SB-223133

CSNK1G3 bound to SB-223133

Entity ID: 1

UniProt & NIH Common Fund Data Resources

Entity Groups

Sequence Annotations