5AIK | pdb_00005aik

Human DYRK1A in complex with LDN-211898

• PDB DOI: https://doi.org/10.2210/pdb5AIK/pdb

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


• Deposited: 2015-02-15 Released: 2015-02-25 
• Deposition Author(s): Elkins, J.M., Soundararajan, M., Muniz, J.R.C., Cuny, G., Higgins, J., Edwards, A., Bountra, C., Knapp, S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free: 
  0.252 (Depositor), 0.255 (DCC) 
• R-Value Work: 
  0.227 (Depositor), 0.230 (DCC) 
• R-Value Observed: 
  0.228 (Depositor) 

Starting Model: experimental

Literature

Dyrk1A with Ldn-211898

Elkins, J.M., Soundararajan, M., Muniz, J.R.C., Cuny, G., Higgins, J., Edwards, A., Bountra, C., 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)

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Biological Assembly 3  

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

Biological assembly 3 assigned by authors and generated by PISA (software)

Biological Assembly 4  

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

Biological assembly 4 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 180.51 kDa 
• Atom Count: 11,321 
• Modeled Residue Count: 1,374 
• Deposited Residue Count: 1,528 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DYRK1A DUAL-SPECIFICITY TYROSINE-PHOSPHORYLATION REGULATED KINASE 1A	A, B, C, D	382	Homo sapiens	Mutation(s): 0  EC: 2.7.11.1 (PDB Primary Data), 2.7.12.1 (UniProt), 2.7.11.23 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for Q13627 (Homo sapiens) Explore Q13627  Go to UniProtKB:  Q13627
PHAROS:  Q13627 GTEx:  ENSG00000157540

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
AWR	E [auth A], H [auth B], L [auth C], O [auth D]	4-(7-METHOXY-1-(TRIFLUOROMETHYL)-9H-PYRIDO[3,4-B]INDOL-9-yl)butan-1-amine C17 H18 F3 N3 O JVBWXORXTBDUMH-UHFFFAOYSA-N
PO4	F [auth A], G [auth A], I [auth B], J [auth B], K [auth B], M [auth C], N [auth C], P [auth D], Q [auth D], R [auth D]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
PTR	A, B, C, D	L-PEPTIDE LINKING	C9 H12 N O6 P		TYR

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free:  0.252 (Depositor), 0.255 (DCC) 
• R-Value Work:  0.227 (Depositor), 0.230 (DCC) 
• R-Value Observed: 0.228 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 89.955	α = 90
b = 90.891	β = 90
c = 232.468	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: 2015-02-25 
Deposition Author(s): Elkins, J.M., Soundararajan, M., Muniz, J.R.C., Cuny, G., Higgins, J., Edwards, A., Bountra, C., Knapp, S.

Revision History  

• Version 1.0: 2015-02-25
  Type: Initial release
  
• Version 1.1: 2018-12-12
  Changes: Data collection, Database references
• Version 1.2: 2021-07-07
  Changes: Derived calculations, Other, Refinement description
• Version 1.3: 2024-01-10
  Changes: Data collection, Database references, Refinement description
• Version 1.4: 2024-10-16
  Changes: Structure summary