3KVW

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)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.28 Å
R-Value Free: 0.260
R-Value Work: 0.209
R-Value Observed: 0.211

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

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.

Macromolecule Content

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

Macromolecules

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(by identity cutoff) | 3D Structure

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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q92630
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
IRB Query on IRB Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A]	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		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain D [auth A] MOL2 format, chain C [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain D [auth A]	C [auth A], D [auth A], E [auth A], F [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A]

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

Binding Affinity Annotations
ID	Source	Binding Affinity
IRB	PDBBind: 3KVW	IC50: 130 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.28 Å
R-Value Free: 0.260
R-Value Work: 0.209
R-Value Observed: 0.211
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

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2010-01-05

Deposition Author(s):

Structural Genomics Consortium (SGC)

Revision History (Full details and data files)

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

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3KVW

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

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

Entity ID: 1

UniProt & NIH Common Fund Data Resources

Entity Groups

Sequence Annotations

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Experimental Data

Structure Validation

Ligand Structure Quality Assessment

Deposition Data

Revision History (Full details and data files)