2JED

The crystal structure of the kinase domain of the protein kinase C theta in complex with NVP-XAA228 at 2.32A resolution.

PDB DOI: https://doi.org/10.2210/pdb2JED/pdb

Classification: TRANSFERASE
Organism(s): Homo sapiens
Mutation(s): Yes

Deposited: 2007-01-16 Released: 2008-02-05
Deposition Author(s): Stark, W., Bitsch, F., Berner, A., Buelens, F., Graff, P., Depersin, H., Geiser, M., Knecht, R., Rahuel, J., Rummel, G., Schlaeppi, J.M., Schmitz, R., Strauss, A., Wagner, J.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.32 Å
R-Value Free: 0.221
R-Value Work: 0.186
R-Value Observed: 0.188

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 Crystal Structure of the Kinase Domain of the Protein Kinase C Theta in Complex with Nvp-Xaa228

Stark, W., Bitsch, F., Berner, A., Buelens, F., Graff, P., Depersin, H., Fendrich, G., Geiser, M., Knecht, R., Rahuel, J., Rummel, G., Schlaeppi, J.M., Schmitz, R., Strauss, A., Wagner, J.

To be published.

Macromolecule Content

Total Structure Weight: 84.67 kDa
Atom Count: 5,884
Modelled Residue Count: 648
Deposited Residue Count: 704
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PROTEIN KINASE C THETA	A, B	352	Homo sapiens	Mutation(s): 2 EC: 2.7.11.13
UniProt & NIH Common Fund Data Resources
Find proteins for Q04759 (Homo sapiens) Explore Q04759 Go to UniProtKB: Q04759
PHAROS: Q04759 GTEx: ENSG00000065675
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q04759
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
LG8 Query on LG8 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]	3-(8-DIMETHYLAMINOMETHYL-6,7,8,9-TETRAHYDRO-PYRIDO[1,2-A]INDOL-10-YL)-4-(1-METHYL-1H-INDOL-3-YL)-PYRROLE-2,5-DIONE C₂₈ H₂₈ N₄ O₂ OYDDKWPGAIBVKO-JQQWWDHGSA-O		Interactions Focus chain C [auth A] Focus chain D [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth B]
MPD Query on MPD Download Ideal Coordinates CCD File SDF format, chain E [auth B] MOL2 format, chain E [auth B] mmCIF format, chain E [auth B]	E [auth B]	(4S)-2-METHYL-2,4-PENTANEDIOL C₆ H₁₄ O₂ SVTBMSDMJJWYQN-YFKPBYRVSA-N		Interactions Focus chain E [auth B] Interactions & Density Focus chain E [auth B]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
SEP Query on SEP	A, B	L-PEPTIDE LINKING	C₃ H₈ N O₆ P		SER

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.32 Å
R-Value Free: 0.221
R-Value Work: 0.186
R-Value Observed: 0.188
Space Group: P 6₅

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 152.172	α = 90
b = 152.172	β = 90
c = 74.837	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling
AMoRE	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2008-02-05

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2008-02-05
Type: Initial release
Version 1.1: 2011-05-08
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Version format compliance
Version 1.3: 2019-05-15
Changes: Data collection, Derived calculations, Experimental preparation, Other
Version 1.4: 2019-09-25
Changes: Data collection, Experimental preparation, Other
Version 1.5: 2023-12-13
Changes: Data collection, Database references, Refinement description
Version 1.6: 2024-10-23
Changes: Structure summary