2J7T | pdb_00002j7t

Crystal structure of human serine threonine kinase-10 bound to SU11274

• PDB DOI: https://doi.org/10.2210/pdb2J7T/pdb

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


• Deposited: 2006-10-17 Released: 2006-11-07 
• Deposition Author(s): Pike, A.C.W., Rellos, P., Fedorov, O., Das, S., Debreczeni, J., Sobott, F., Watt, S., Savitsky, P., Eswaran, J., Turnbull, A.P., Papagrigoriou, E., Ugochukwa, E., Gorrec, F., Umeano, C.C., von Delft, F., Arrowsmith, C.H., Edwards, A., Weigelt, J., Sundstrom, M., Knapp, S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.235 (Depositor), 0.230 (DCC) 
• R-Value Work: 
  0.204 (Depositor), 0.205 (DCC) 
• R-Value Observed: 
  0.205 (Depositor) 

Starting Model: experimental

Literature

Activation Segment Dimerization: A Mechanism for Kinase Autophosphorylation of Non-Consensus Sites.

Pike, A.C.W., Rellos, P., Niesen, F.H., Turnbull, A., Oliver, A.W., Parker, S.A., Turk, B.E., Pearl, L.H., Knapp, S.

(2008) EMBO J 27: 704

• PubMed: 18239682 
• DOI: https://doi.org/10.1038/emboj.2008.8
• Primary Citation Related Structures: 
  2J51, 2J7T, 2J90, 2JFL, 2JFM, 2UV2


• PubMed Abstract: 
  

  Protein kinase autophosphorylation of activation segment residues is a common regulatory mechanism in phosphorylation-dependent signalling cascades. However, the molecular mechanisms that guarantee specific and efficient phosphorylation of these sites have not been elucidated. Here, we report on three novel and diverse protein kinase structures that reveal an exchanged activation segment conformation. This dimeric arrangement results in an active kinase conformation in trans, with activation segment phosphorylation sites in close proximity to the active site of the interacting protomer. Analytical ultracentrifugation and chemical cross-linking confirmed the presence of dimers in solution. Consensus substrate sequences for each kinase showed that the identified activation segment autophosphorylation sites are non-consensus substrate sites. Based on the presented structural and functional data, a model for specific activation segment phosphorylation at non-consensus substrate sites is proposed that is likely to be common to other kinases from diverse subfamilies.

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Organizational Affiliation: 
• Structural Genomics Consortium, Botnar Research Centre, University of Oxford, Oxford, UK.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PQS (software)

Macromolecule Content 

• Total Structure Weight: 35.21 kDa 
• Atom Count: 2,342 
• Modeled Residue Count: 285 
• Deposited Residue Count: 302 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
SERINE/THREONINE-PROTEIN KINASE 10	A	302	Homo sapiens	Mutation(s): 0  EC: 2.7.11.1
UniProt & NIH Common Fund Data Resources
Find proteins for O94804 (Homo sapiens) Explore O94804  Go to UniProtKB:  O94804
PHAROS:  O94804 GTEx:  ENSG00000072786

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
274	J [auth A]	(3Z)-N-(3-CHLOROPHENYL)-3-({3,5-DIMETHYL-4-[(4-METHYLPIPERAZIN-1-YL)CARBONYL]-1H-PYRROL-2-YL}METHYLENE)-N-METHYL-2-OXOINDOLINE-5-SULFONAMIDE C28 H30 Cl N5 O4 S FPYJSJDOHRDAMT-KQWNVCNZSA-N
ACT	I [auth A]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M
CA	B [auth A], C [auth A], D [auth A], E [auth A], F [auth A], G [auth A], H [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.235 (Depositor), 0.230 (DCC) 
• R-Value Work:  0.204 (Depositor), 0.205 (DCC) 
• R-Value Observed: 0.205 (Depositor) 

Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 49.192	α = 90
b = 112.96	β = 90
c = 133.817	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2006-11-07 
Deposition Author(s): Pike, A.C.W., Rellos, P., Fedorov, O., Das, S., Debreczeni, J., Sobott, F., Watt, S., Savitsky, P., Eswaran, J., Turnbull, A.P., Papagrigoriou, E., Ugochukwa, E., Gorrec, F., Umeano, C.C., von Delft, F., Arrowsmith, C.H., Edwards, A., Weigelt, J., Sundstrom, M., Knapp, S.

Revision History  

• Version 1.0: 2006-11-07
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 1.2: 2018-06-27
  Changes: Data collection, Derived calculations
• Version 1.3: 2023-12-13
  Changes: Data collection, Database references, Derived calculations, Other, Refinement description
• Version 1.4: 2024-11-20
  Changes: Structure summary