9N2M | pdb_00009n2m

Crystal Structure of Human DAPK1 Catalytic Subunit Complexed with Compound MW01-30-047SRM

PDB DOI: https://doi.org/10.2210/pdb9N2M/pdb

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

Deposited: 2025-01-29 Released: 2025-04-02
Deposition Author(s): Brunzelle, J.S., Shuvalova, L., Roy, S.M., Watterson, D.M.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.35 Å
R-Value Free:
0.177 (Depositor), 0.182 (DCC)
R-Value Work:
0.144 (Depositor), 0.156 (DCC)
R-Value Observed:
0.146 (Depositor)

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Ligand Structure Quality Assessment

This is version 1.0 of the entry. See complete history.

Literature

Crystal Structure of Human DAPK1 Catalytic Subunit Complexed with Compound MW01-30-047SRM

Brunzelle, J.S., Shuvalova, L., Roy, S.M., Watterson, D.M.

To be published.

Macromolecule Content

Total Structure Weight: 34.08 kDa
Atom Count: 2,606
Modeled Residue Count: 280
Deposited Residue Count: 293
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Death-associated protein kinase 1	A	293	Homo sapiens	Mutation(s): 0 Gene Names: DAPK1, DAPK EC: 2.7.11.1
UniProt & NIH Common Fund Data Resources
Find proteins for P53355 (Homo sapiens) Explore P53355 Go to UniProtKB: P53355
PHAROS: P53355 GTEx: ENSG00000196730
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P53355
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
A1BVM Query on A1BVM Download:Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	5-(pyridin-4-yl)-3-[4-(pyridin-4-yl)piperazin-1-yl]pyridazine C₁₈ H₁₈ N₆ PMYQZDHMSFEWMS-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.35 Å
R-Value Free: 0.177 (Depositor), 0.182 (DCC)
R-Value Work: 0.144 (Depositor), 0.156 (DCC)
R-Value Observed: 0.146 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 47.3	α = 90
b = 63.08	β = 90
c = 88.12	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
Aimless	data scaling
xia2	data reduction
REFMAC	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2025-04-02

Deposition Author(s):

Brunzelle, J.S.

Watterson, D.M.

Funding Organization	Location	Grant Number
Not funded		--

Revision History (Full details and data files)

Version 1.0: 2025-04-02
Type: Initial release

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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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.