3GU8 | pdb_00003gu8

Crystal structure of DAPKL93G with N6-cyclopentyladenosine

PDB DOI: https://doi.org/10.2210/pdb3GU8/pdb

Classification: TRANSFERASE
Organism(s): Homo sapiens
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2009-03-28 Released: 2010-03-09
Deposition Author(s): McNamara, L.K., Schumacher, A.M., Schavocky, J.S., Watterson, D.M., Brunzelle, J.S.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.60 Å
R-Value Free:
0.239 (Depositor), 0.240 (DCC)
R-Value Work:
0.201 (Depositor), 0.200 (DCC)
R-Value Observed:
0.203 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

Literature

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

McNamara, L.K., Schavocky, J.S., Watterson, D.M., Brunzelle, J.S.

To be published.

Macromolecule Content

Total Structure Weight: 34.2 kDa
Atom Count: 2,590
Modeled Residue Count: 278
Deposited Residue Count: 295
Unique protein chains: 1

Macromolecules

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(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 Gene Names: DAPK, DAPK1, death-associated protein kinase 1 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% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P53355
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
3GU Query on 3GU 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]	N6-cyclopentyladenosine C₁₅ H₂₁ N₅ O₄ SQMWSBKSHWARHU-SDBHATRESA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.60 Å
R-Value Free: 0.239 (Depositor), 0.240 (DCC)
R-Value Work: 0.201 (Depositor), 0.200 (DCC)
R-Value Observed: 0.203 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 47.109	α = 90
b = 62.745	β = 90
c = 88.785	γ = 90

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2010-03-09

Deposition Author(s):

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.