3KVW | pdb_00003kvw

Crystal Structure of dual-specificity tyrosine phosphorylation regulated kinase 2 (DYRK2) in complex with an indirubin ligand

• PDB DOI: https://doi.org/10.2210/pdb3KVW/pdb

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


• Deposited: 2009-11-30 Released: 2010-01-05 
• Deposition Author(s): Filippakopoulos, P., Myrianthopoulos, V., Kritsanida, M., Magiatis, P., Skaltsounis, A.L., Soundararajan, M., Krojer, T., Gileadi, O., Hapka, E., Fedorov, O., Berridge, G., Wang, J., Shrestha, L., Vollmar, M., von Delft, F., Arrowsmith, C.H., Edwards, A., Weigelt, J., Bountra, C., Mikros, E., Knapp, S., Structural Genomics Consortium (SGC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.28 Å
• R-Value Free: 
  0.260 (Depositor), 0.262 (DCC) 
• R-Value Work: 
  0.209 (Depositor), 0.211 (DCC) 
• R-Value Observed: 
  0.211 (Depositor) 

Starting Model: experimental

Literature

Crystal Structure of dual-specificity tyrosine phosphorylation regulated kinase 2 (DYRK2) in complex with an indirubin ligand

Filippakopoulos, P., Myrianthopoulos, V., Kritsanida, M., Magiatis, P., Skaltsounis, A.L., Soundararajan, M., Krojer, T., Gileadi, O., Hapka, E., Fedorov, O., Berridge, G., Wang, J., Shrestha, L., Vollmar, M., von Delft, F., Arrowsmith, C.H., Edwards, A., Weigelt, J., Bountra, C., Mikros, E., Knapp, S.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Macromolecule Content 

• Total Structure Weight: 50.14 kDa 
• Atom Count: 3,375 
• Modeled Residue Count: 406 
• Deposited Residue Count: 429 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Dual specificity tyrosine-phosphorylation-regulated kinase 2	A	429	Homo sapiens	Mutation(s): 0  Gene Names: DYRK2 EC: 2.7.12.1
UniProt & NIH Common Fund Data Resources
Find proteins for Q92630 (Homo sapiens) Explore Q92630  Go to UniProtKB:  Q92630
PHAROS:  Q92630 GTEx:  ENSG00000127334

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
IRB	B [auth A]	(2Z,3E)-7'-bromo-3-(hydroxyimino)-2'-oxo-1,1',2',3-tetrahydro-2,3'-biindole-5-carboxylic acid C17 H10 Br N3 O4 UHBJSHHMZNYBAE-HQMCVCOQSA-N
CL	C [auth A], D [auth A], E [auth A], F [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Modified Residues  2 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
PTR	A	L-PEPTIDE LINKING	C9 H12 N O6 P		TYR
SEP	A	L-PEPTIDE LINKING	C3 H8 N O6 P		SER

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.28 Å
• R-Value Free:  0.260 (Depositor), 0.262 (DCC) 
• R-Value Work:  0.209 (Depositor), 0.211 (DCC) 
• R-Value Observed: 0.211 (Depositor) 

Space Group: P 4₂ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 84.28	α = 90
b = 84.28	β = 90
c = 149.12	γ = 90

Software Package:

Software Name	Purpose
SCALA	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
GDA	data collection
MOSFLM	data reduction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-01-05 
Deposition Author(s): Filippakopoulos, P., Myrianthopoulos, V., Kritsanida, M., Magiatis, P., Skaltsounis, A.L., Soundararajan, M., Krojer, T., Gileadi, O., Hapka, E., Fedorov, O., Berridge, G., Wang, J., Shrestha, L., Vollmar, M., von Delft, F., Arrowsmith, C.H., Edwards, A., Weigelt, J., Bountra, C., Mikros, E., Knapp, S., Structural Genomics Consortium (SGC)

Revision History  

• Version 1.0: 2010-01-05
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 1.2: 2023-11-01
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.3: 2023-11-22
  Changes: Data collection
• Version 1.4: 2024-10-09
  Changes: Structure summary