7CCU | pdb_00007ccu

Crystal structure of death-associated protein kinase 1 in complex with resveratrol

PDB DOI: https://doi.org/10.2210/pdb7CCU/pdb

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

Deposited: 2020-06-18 Released: 2021-01-20
Deposition Author(s): Yokoyama, T., Suzuki, R., Mizuguchi, M.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.65 Å
R-Value Free:
0.199 (Depositor), 0.200 (DCC)
R-Value Work:
0.175 (Depositor), 0.170 (DCC)
R-Value Observed:
0.176 (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 death-associated protein kinase 1 in complex with the dietary compound resveratrol.

Yokoyama, T., Suzuki, R., Mizuguchi, M.

(2020) IUCrJ 8: 131-138

DOI: https://doi.org/10.1107/S2052252520015614

Macromolecule Content

Total Structure Weight: 34.12 kDa
Atom Count: 2,487
Modeled Residue Count: 276
Deposited Residue Count: 293
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	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% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P53355
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
STL (Subject of Investigation/LOI) Query on STL 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]	RESVERATROL C₁₄ H₁₂ O₃ LUKBXSAWLPMMSZ-OWOJBTEDSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
SO4 Query on SO4 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]	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: X-RAY DIFFRACTION
Resolution: 1.65 Å
R-Value Free: 0.199 (Depositor), 0.200 (DCC)
R-Value Work: 0.175 (Depositor), 0.170 (DCC)
R-Value Observed: 0.176 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 46.888	α = 90
b = 62.234	β = 90
c = 88.248	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling
PHENIX	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2021-01-20

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2021-01-20
Type: Initial release
Version 1.1: 2023-11-29
Changes: Data collection, Database references, 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.