3GUB | pdb_00003gub

Crystal structure of DAPKL93G complexed with N6-(2-Phenylethyl)adenosine

PDB DOI:&nbsphttps://doi.org/10.2210/pdb3GUB/pdb

Classification:&nbspTRANSFERASE
Organism(s):&nbspHomo sapiens
Expression System:&nbspEscherichia coli
Mutation(s):&nbspYes&nbsp

Deposited:&nbsp2009-03-29&nbspReleased:&nbsp2010-03-09&nbsp
Deposition Author(s):&nbspMcNamara, L.K., Schumacher, A.M., Schavocky, J.S., Watterson, D.M., Brunzelle, J.S.

Experimental Data Snapshot

Method:&nbspX-RAY DIFFRACTION
Resolution:&nbsp1.71 Å
R-Value Free:&nbsp
0.239 (Depositor), 0.240 (DCC)&nbsp
R-Value Work:&nbsp
0.195 (Depositor), 0.190 (DCC)&nbsp
R-Value Observed:&nbsp
0.197&nbsp(Depositor)&nbsp

Starting Model: experimental
View more details

wwPDB Validation&nbsp 3D Report&nbspFull Report

Ligand Structure Quality Assessment&nbsp

This is version 1.3 of the entry. See complete&nbsphistory.&nbsp

Literature

Crystal structures of the DAPK gatekeeper mutant complexed with N6-modified adenosine analogs.

McNamara, L.K.,&nbspSchavocky, J.S.,&nbspWatterson, D.M.,&nbspBrunzelle, J.S.

To be published.

Macromolecule Content

Total Structure Weight: 34.34 kDa&nbsp
Atom Count: 2,522&nbsp
Modelled Residue Count: 278&nbsp
Deposited Residue Count: 295&nbsp
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Death-associated protein kinase 1	A	295	Homo sapiens	Mutation(s): 1&nbsp Gene Names:&nbspDAPK,&nbspDAPK1,&nbspdeath-associated protein kinase 1 EC:&nbsp2.7.11.1
UniProt & NIH Common Fund Data Resources
Find proteins for&nbspP53355&nbsp(Homo sapiens) Explore&nbspP53355&nbsp Go to UniProtKB: &nbspP53355
PHAROS: &nbspP53355 GTEx: &nbspENSG00000196730&nbsp
Entity Groups &nbsp
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P53355
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands&nbsp2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GUB Query on GUB Download Ideal Coordinates CCD File&nbsp SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	9-alpha-L-lyxofuranosyl-N-(2-phenylethyl)-9H-purin-6-amine C₁₈ H₂₁ N₅ O₄ LGZYEDZSPHLISU-KDQZPGIASA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
SO4 Query on SO4 Download Ideal Coordinates CCD File&nbsp SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]

Experimental Data & Validation

Experimental Data

Method:&nbspX-RAY DIFFRACTION
Resolution:&nbsp1.71 Å
R-Value Free:&nbsp 0.239 (Depositor), 0.240 (DCC)&nbsp
R-Value Work:&nbsp 0.195 (Depositor), 0.190 (DCC)&nbsp
R-Value Observed:&nbsp0.197&nbsp(Depositor)&nbsp

Space Group:&nbspP 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 46.839	α = 90
b = 62.881	β = 90
c = 88.467	γ = 90

Software Package:

Software Name	Purpose
MOLREP	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

View&nbspFull Validation Report

Ligand Structure Quality Assessment&nbsp

Entry History&nbsp

Deposition Data

Released Date:&nbsp2010-03-09&nbsp

Deposition Author(s):&nbsp

Schumacher, A.M.

Schavocky, J.S.

Watterson, D.M.

Brunzelle, J.S.

Revision History (Full details and data files)

Version 1.0: 2010-03-09
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2021-10-13
Changes: Database references, Derived calculations
Version 1.3: 2023-09-06
Changes: Data collection, Refinement description

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.