8C3Q | pdb_00008c3q

Crystal structure of DYRK1A in complex with rutin

PDB DOI: https://doi.org/10.2210/pdb8C3Q/pdb

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

Deposited: 2022-12-28 Released: 2024-01-10
Deposition Author(s): Grygier, P., Pustelny, K., Dubin, G., Czarna, A.
Funding Organization(s): Polish National Science Centre, National Center for Research and Development (Poland)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.32 Å
R-Value Free:
0.210 (Depositor), 0.210 (DCC)
R-Value Work:
0.177 (Depositor), 0.180 (DCC)
R-Value Observed:
0.178 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

Crystal structure of DYRK1A in complex with rutin

Grygier, P., Pustelny, K., Dubin, G., Czarna, A.

To be published.

Macromolecule Content

Total Structure Weight: 87.58 kDa
Atom Count: 5,746
Modeled Residue Count: 688
Deposited Residue Count: 740
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 1A	A, B	370	Homo sapiens	Mutation(s): 0 Gene Names: DYRK1A, DYRK, MNB, MNBH EC: 2.7.12.1 (PDB Primary Data), 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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q13627
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
RUT (Subject of Investigation/LOI) Query on RUT Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [auth B] mmCIF format, chain C [auth A] mmCIF format, chain D [auth B]	C [auth A], D [auth B]	RUTIN C₂₇ H₃₀ O₁₆ IKGXIBQEEMLURG-NVPNHPEKSA-N		Interactions Focus chain C [auth A] Focus chain D [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth B]

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

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.32 Å
R-Value Free: 0.210 (Depositor), 0.210 (DCC)
R-Value Work: 0.177 (Depositor), 0.180 (DCC)
R-Value Observed: 0.178 (Depositor)

Space Group: P 6₃

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 134.187	α = 90
b = 134.187	β = 90
c = 91.15	γ = 120

Software Package:

Software Name	Purpose
Aimless	data scaling
PHENIX	refinement
XDS	data reduction
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2024-01-10

Deposition Author(s):

Funding Organization	Location	Grant Number
Polish National Science Centre	Poland	2019/34/E/NZ1/00467
National Center for Research and Development (Poland)	Poland	PPN/PPO/2018/1/00046

Revision History (Full details and data files)

Version 1.0: 2024-01-10
Type: Initial release
Version 1.1: 2024-11-06
Changes: Structure summary

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.