1WVY | pdb_00001wvy

Crystal structures of kinase domain of DAP kinase in complex with small molecular inhibitors

PDB DOI: https://doi.org/10.2210/pdb1WVY/pdb

Classification: TRANSFERASE
Organism(s): Homo sapiens
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2004-12-27 Released: 2006-04-11
Deposition Author(s): Ueda, Y., Ogata, H., Yamakawa, A., Higuchi, Y.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.80 Å
R-Value Free:
0.274 (Depositor)
R-Value Work:
0.213 (Depositor)
R-Value Observed:
0.222 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 1WVY

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

Literature

Complex structure of kinase domain of DAP kinase with Staurosporine

Ueda, Y., Ogata, H., Yamakawa, A., Higuchi, Y.

To be published.

Macromolecule Content

Total Structure Weight: 32.45 kDa
Atom Count: 2,385
Modeled Residue Count: 273
Deposited Residue Count: 278
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Death-associated protein kinase 1	A	278	Homo sapiens	Mutation(s): 0 EC: 2.7.1.37 (PDB Primary Data), 2.7.11.1 (UniProt)
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 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
STU Query on STU 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]	STAUROSPORINE C₂₈ H₂₆ N₄ O₃ HKSZLNNOFSGOKW-FYTWVXJKSA-N		Interactions Focus chain B [auth A]

Binding Affinity Annotations
ID	Source	Binding Affinity
STU	BindingDB: 1WVY	IC50: 1 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.80 Å
R-Value Free: 0.274 (Depositor)
R-Value Work: 0.213 (Depositor)
R-Value Observed: 0.222 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 78.911	α = 90
b = 113.162	β = 90
c = 50.658	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
MOSFLM	data reduction
CCP4	data scaling
CNS	phasing

Structure Validation

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View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2006-04-11

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2006-04-11
Type: Initial release
Version 1.1: 2008-04-30
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Version format compliance
Version 1.3: 2024-03-13
Changes: Data collection, Database references, Derived calculations

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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.