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), 0.199 (DCC)
R-Value Work:
0.175 (Depositor), 0.175 (DCC)
R-Value Observed:
0.176 (Depositor)

Starting Model: experimental
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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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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
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), 0.199 (DCC)
R-Value Work: 0.175 (Depositor), 0.175 (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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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

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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.