3BHH | pdb_00003bhh

Crystal structure of human calcium/calmodulin-dependent protein kinase IIB isoform 1 (CAMK2B)

PDB DOI: https://doi.org/10.2210/pdb3BHH/pdb

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

Deposited: 2007-11-28 Released: 2007-12-11
Deposition Author(s): Filippakopoulos, P., Rellos, P., Niesen, F., Burgess, N., Bullock, A., Berridge, G., Pike, A.C.W., Ugochukwu, E., Pilka, E.S., von Delft, F., Arrowsmith, C.H., Edwards, A.M., Weigelt, J., Knapp, S., Structural Genomics Consortium (SGC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.40 Å
R-Value Free:
0.275 (Depositor)
R-Value Work:
0.223 (Depositor), 0.228 (DCC)
R-Value Observed:
0.225 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Crystal Structure of Human Calcium/Calmodulin-Dependent Protein Kinase IIB Isoform 1 (CAMK2B).

Filippakopoulos, P., Rellos, P., Niesen, F., Burgess, N., Bullock, A., Berridge, G., Pike, A.C.W., Ugochukwu, E., Pilka, E.S., von Delft, F., Arrowsmith, C.H., Edwards, A.M., Weigelt, J., Knapp, S.

To be published.

Macromolecule Content

Total Structure Weight: 134.98 kDa
Atom Count: 8,933
Modeled Residue Count: 1,149
Deposited Residue Count: 1,180
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Calcium/calmodulin-dependent protein kinase type II beta chain	A, B, C, D	295	Homo sapiens	Mutation(s): 0 Gene Names: CAMK2B, CAM2, CAMKB EC: 2.7.11.17
UniProt & NIH Common Fund Data Resources
Find proteins for Q13554 (Homo sapiens) Explore Q13554 Go to UniProtKB: Q13554
PHAROS: Q13554 GTEx: ENSG00000058404
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q13554
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
5CP Query on 5CP Download:Ideal Coordinates CCD File SDF format, chain F [auth B] SDF format, chain E [auth A] MOL2 format, chain F [auth B] MOL2 format, chain E [auth A] mmCIF format, chain F [auth B] mmCIF format, chain E [auth A]	E [auth A], F [auth B]	[4-({4-[(5-cyclopropyl-1H-pyrazol-3-yl)amino]-6-(methylamino)pyrimidin-2-yl}amino)phenyl]acetonitrile C₁₉ H₂₀ N₈ MFMSRHREFZCFSN-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain F [auth B] Interactions & Density Focus chain E [auth A] Focus chain F [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.40 Å
R-Value Free: 0.275 (Depositor)
R-Value Work: 0.223 (Depositor), 0.228 (DCC)
R-Value Observed: 0.225 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 173.4	α = 90
b = 79.2	β = 104.5
c = 98.7	γ = 90

Software Package:

Software Name	Purpose
PHASER	phasing
DM	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
CrystalClear	data collection
XDS	data reduction
XDS	data scaling

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2007-12-11

Deposition Author(s):

Structural Genomics Consortium (SGC)

Revision History (Full details and data files)

Version 1.0: 2007-12-11
Type: Initial release
Version 1.1: 2011-07-13
Changes: Advisory, Version format compliance
Version 1.2: 2023-08-30
Changes: Data collection, Database references, Derived calculations, Refinement description