2JC6

Crystal structure of human calmodulin-dependent protein kinase 1D

PDB DOI: https://doi.org/10.2210/pdb2JC6/pdb

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

Deposited: 2006-12-19 Released: 2007-02-13
Deposition Author(s): Debreczeni, J.E., Rellos, P., Fedorov, O., Niesen, F.H., Bhatia, C., Shrestha, L., Salah, E., Smee, C., Colebrook, S., Berridge, G., Gileadi, O., Bunkoczi, G., Ugochukwu, E., Pike, A.C.W., von Delft, F., Knapp, S., Sundstrom, M., Weigelt, J., Arrowsmith, C.H., Edwards, A.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free: 0.248
R-Value Work: 0.186
R-Value Observed: 0.189

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Crystal Structure of Human Calmodulin-Dependent Protein Kinase 1D

Debreczeni, J.E., Rellos, P., Fedorov, O., Niesen, F.H., Bhatia, C., Shrestha, L., Salah, E., Smee, C., Colebrook, S., Berridge, G., Gileadi, O., Bunkoczi, G., Ugochukwu, E., Pike, A.C.W., von Delft, F., Knapp, S., Sundstrom, M., Weigelt, J., Arrowsmith, C.H., Edwards, A.

To be published.

Macromolecule Content

Total Structure Weight: 76.38 kDa
Atom Count: 4,628
Modelled Residue Count: 555
Deposited Residue Count: 668
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
CALCIUM/CALMODULIN-DEPENDENT PROTEIN KINASE TYPE 1D	A, B [auth C]	334	Homo sapiens	Mutation(s): 0 EC: 2.7.11.17
UniProt & NIH Common Fund Data Resources
Find proteins for Q8IU85 (Homo sapiens) Explore Q8IU85 Go to UniProtKB: Q8IU85
PHAROS: Q8IU85 GTEx: ENSG00000183049
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q8IU85
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
QPP Query on QPP Download Ideal Coordinates CCD File SDF format, chain D [auth C] SDF format, chain C [auth A] MOL2 format, chain D [auth C] MOL2 format, chain C [auth A]	C [auth A], D [auth C]	N-(5-METHYL-1H-PYRAZOL-3-YL)-2-PHENYLQUINAZOLIN-4-AMINE C₁₈ H₁₅ N₅ JYCUVOXSZBECAY-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth C] Interactions & Density Focus chain C [auth A] Focus chain D [auth C]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free: 0.248
R-Value Work: 0.186
R-Value Observed: 0.189
Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 39.64	α = 90
b = 93.06	β = 96.16
c = 101.86	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

Entry History

Deposition Data

Released Date: 2007-02-13

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2007-02-13
Type: Initial release
Version 1.1: 2011-07-13
Changes: Refinement description, Version format compliance
Version 1.2: 2018-01-24
Changes: Database references
Version 1.3: 2023-12-13
Changes: Data collection, Database references, Other, Refinement description

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2JC6

Crystal structure of human calmodulin-dependent protein kinase 1D

Crystal Structure of Human Calmodulin-Dependent Protein Kinase 1D

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)