2C47 | pdb_00002c47

Structure of casein kinase 1 gamma 2

PDB DOI: https://doi.org/10.2210/pdb2C47/pdb

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

Deposited: 2005-10-16 Released: 2005-11-07
Deposition Author(s): Bunkoczi, G., Rellos, P., Das, S., Ugochukwu, E., Fedorov, O., Sobott, F., Eswaran, J., Amos, A., Ball, L., von Delft, F., Bullock, A., Debreczeni, J., Turnbull, A., Sundstrom, M., Weigelt, J., Arrowsmith, C., Edwards, A., Knapp, S.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.40 Å
R-Value Free:
0.257 (Depositor), 0.263 (DCC)
R-Value Work:
0.208 (Depositor), 0.216 (DCC)
R-Value Observed:
0.211 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.6 of the entry. See complete history.

Literature

The Structure of Casein Kinase 1 Gamma 2

Bunkoczi, G., Rellos, P., Das, S., Ugochukwu, E., Fedorov, O., Sobott, F., Eswaran, J., Amos, A., Ball, L., von Delft, F., Bullock, A., Debreczeni, J., Turnbull, A., Sundstrom, M., Weigelt, J., Arrowsmith, C., Edwards, A., Knapp, S.

To be published.

Macromolecule Content

Total Structure Weight: 147.99 kDa
Atom Count: 9,545
Modeled Residue Count: 1,153
Deposited Residue Count: 1,252
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
CASEIN KINASE 1 GAMMA 2 ISOFORM	A, B, C, D	313	Homo sapiens	Mutation(s): 0 EC: 2.7.1 (PDB Primary Data), 2.7.11.1 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for P78368 (Homo sapiens) Explore P78368 Go to UniProtKB: P78368
PHAROS: P78368 GTEx: ENSG00000133275
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P78368
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
5ID Query on 5ID Download:Ideal Coordinates CCD File SDF format, chain J [auth D] SDF format, chain H [auth C] SDF format, chain F [auth B] SDF format, chain E [auth A] MOL2 format, chain J [auth D] MOL2 format, chain H [auth C] MOL2 format, chain F [auth B] MOL2 format, chain E [auth A] mmCIF format, chain J [auth D] mmCIF format, chain H [auth C] mmCIF format, chain F [auth B] mmCIF format, chain E [auth A]	E [auth A], F [auth B], H [auth C], J [auth D]	(2R,3R,4S,5R)-2-(4-AMINO-5-IODO-7H-PYRROLO[2,3-D]PYRIMIDIN-7-YL)-5-(HYDROXYMETHYL)TETRAHYDROFURAN-3,4-DIOL C₁₁ H₁₃ I N₄ O₄ WHSIXKUPQCKWBY-IOSLPCCCSA-N		Interactions Focus chain E [auth A] Focus chain F [auth B] Focus chain H [auth C] Focus chain J [auth D] Interactions & Density Focus chain E [auth A] Focus chain F [auth B] Focus chain H [auth C] Focus chain J [auth D]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain I [auth C] SDF format, chain G [auth B] MOL2 format, chain I [auth C] MOL2 format, chain G [auth B] mmCIF format, chain I [auth C] mmCIF format, chain G [auth B]	G [auth B], I [auth C]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain G [auth B] Focus chain I [auth C] Interactions & Density Focus chain G [auth B] Focus chain I [auth C]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
CSD Query on CSD	A, B, C, D	L-PEPTIDE LINKING	C₃ H₇ N O₄ S		CYS

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.40 Å
R-Value Free: 0.257 (Depositor), 0.263 (DCC)
R-Value Work: 0.208 (Depositor), 0.216 (DCC)
R-Value Observed: 0.211 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 93.959	α = 90
b = 97.088	β = 90
c = 185.914	γ = 90

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2005-11-07

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2005-11-07
Type: Initial release
Version 1.1: 2011-07-13
Changes: Advisory, Refinement description, Version format compliance
Version 1.2: 2012-08-22
Changes: Atomic model, Database references, Derived calculations, Non-polymer description, Other, Refinement description
Version 1.3: 2018-01-24
Changes: Database references
Version 1.4: 2018-02-28
Changes: Source and taxonomy
Version 1.5: 2023-12-13
Changes: Data collection, Database references, Derived calculations, Other, Refinement description
Version 1.6: 2024-11-06
Changes: Structure summary