4YPD

Crystal Structure of DAPK1 catalytic domain in complex with the hinge binding fragment 4-methylpyridazine


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.4 Å
  • R-Value Free: 0.177 
  • R-Value Work: 0.155 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Crystal Structure of DAPK1 catalytic domain in complex with hinge binding fragments

Grum-Tokars, V.L.Minasov, G.Roy, S.M.Anderson, W.F.Watterson, D.M.

To be published.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Death-associated protein kinase 1
A
294Homo sapiensMutation(s): 0 
Gene Names: DAPK1 (DAPK)
EC: 2.7.11.1
Find proteins for P53355 (Homo sapiens)
Go to Gene View: DAPK1
Go to UniProtKB:  P53355
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
DKG
Query on DKG

Download SDF File 
Download CCD File 
A
4-methylpyridazine
C5 H6 N2
AIKUBOPKWKZULG-UHFFFAOYSA-N
 Ligand Interaction
SO4
Query on SO4

Download SDF File 
Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
CL
Query on CL

Download SDF File 
Download CCD File 
A
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.4 Å
  • R-Value Free: 0.177 
  • R-Value Work: 0.155 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 46.853α = 90.00
b = 62.511β = 90.00
c = 88.193γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data scaling
PHASERphasing
HKL-2000data reduction
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute on Aging (NIH/NIA)United StatesU01AG043415

Revision History 

  • Version 1.0: 2015-05-13
    Type: Initial release
  • Version 1.1: 2017-09-06
    Type: Advisory, Author supporting evidence, Database references, Derived calculations, Other, Source and taxonomy
  • Version 1.2: 2019-12-18
    Type: Author supporting evidence