5HTC | pdb_00005htc

Crystal structure of haspin (GSG2) in complex with bisubstrate inhibitor ARC-3372

• PDB DOI: https://doi.org/10.2210/pdb5HTC/pdb

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


• Deposited: 2016-01-26 Released: 2016-03-16 
• Deposition Author(s): Chaikuad, A., Heroven, C., Lavogina, D., Kestav, K., Uri, A., von Delft, F., Arrowsmith, C.H., Edwards, A.M., Bountra, C., Knapp, S., Structural Genomics Consortium (SGC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 
  0.171 (Depositor), 0.172 (DCC) 
• R-Value Work: 
  0.150 (Depositor), 0.149 (DCC) 
• R-Value Observed: 
  0.151 (Depositor) 

Starting Model: experimental

Literature

Co-crystal structures of the protein kinase haspin with bisubstrate inhibitors.

Lavogina, D., Kestav, K., Chaikuad, A., Heroven, C., Knapp, S., Uri, A.

(2016) Acta Crystallogr F Struct Biol Commun 72: 339-345

• PubMed: 27139824 
• DOI: https://doi.org/10.1107/S2053230X16004611
• Primary Citation Related Structures: 
  5HTB, 5HTC


• PubMed Abstract: 
  

  Haspin is a mitotic protein kinase that is responsible for the phosphorylation of Thr3 of histone H3, thereby creating a recognition motif for docking of the chromosomal passenger complex that is crucial for the progression of cell division. Here, two high-resolution models of haspin with previously reported inhibitors consisting of an ATP analogue and a histone H3(1-7) peptide analogue are presented. The structures of the complexes confirm the bisubstrate character of the inhibitors by revealing the signature binding modes of the moieties targeting the ATP-binding site and the protein substrate-binding site of the kinase. This is the first structural model of a bisubstrate inhibitor targeting haspin. The presented structural data represent a model for the future development of more specific haspin inhibitors.

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Organizational Affiliation: 
• Institute of Chemistry, University of Tartu, Ravila 14A, 50411 Tartu, Estonia.
Nuffield Department of Clinical Medicine, Structural Genomics Consortium, University of Oxford, Old Road Campus Research Building, Oxford OX3 7DQ, England.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 42.36 kDa 
• Atom Count: 3,346 
• Modeled Residue Count: 335 
• Deposited Residue Count: 364 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Serine/threonine-protein kinase haspin	A	357	Homo sapiens	Mutation(s): 0  Gene Names: GSG2 EC: 2.7.11.1
UniProt & NIH Common Fund Data Resources
Find proteins for Q8TF76 (Homo sapiens) Explore Q8TF76  Go to UniProtKB:  Q8TF76
PHAROS:  Q8TF76 GTEx:  ENSG00000177602

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
ARC-3372 INHIBITOR	B [auth C]	7	synthetic construct	Mutation(s): 0

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
66M	G [auth C]	(2R)-2-{[6-({[(2S,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxytetrahydrofuran-2-yl]carbonyl}amino)hexanoyl]amino}butanedioic acid (non-preferred name) C20 H27 N7 O9 MMQKVHWBTLHGSP-ZXQBGJJXSA-N
MPD	C [auth A], D [auth A]	(4S)-2-METHYL-2,4-PENTANEDIOL C6 H14 O2 SVTBMSDMJJWYQN-YFKPBYRVSA-N
DMS	F [auth A]	DIMETHYL SULFOXIDE C2 H6 O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N
NA	E [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free:  0.171 (Depositor), 0.172 (DCC) 
• R-Value Work:  0.150 (Depositor), 0.149 (DCC) 
• R-Value Observed: 0.151 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 77.97	α = 90
b = 78.903	β = 90
c = 81.06	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-03-16 
Deposition Author(s): Chaikuad, A., Heroven, C., Lavogina, D., Kestav, K., Uri, A., von Delft, F., Arrowsmith, C.H., Edwards, A.M., Bountra, C., Knapp, S., Structural Genomics Consortium (SGC)

Revision History  

• Version 1.0: 2016-03-16
  Type: Initial release
  
• Version 1.1: 2016-05-04
  Changes: Database references
• Version 1.2: 2016-05-11
  Changes: Database references
• Version 1.3: 2018-01-24
  Changes: Source and taxonomy
• Version 1.4: 2024-02-07
  Changes: Data collection, Database references, Derived calculations, Refinement description