Macromolecule Content

Total Structure Weight: 32.3 kDa
Atom Count: 2,329
Modelled Residue Count: 275
Deposited Residue Count: 278
Unique protein chains: 1

1WVX

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

PDB DOI: 10.2210/pdb1WVX/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: 2.60 Å
R-Value Free: 0.270
R-Value Work: 0.225
R-Value Observed: 0.225

wwPDB Validation 3D Report Full Report

This is version 1.2 of the entry. See complete history.

Literature

Complex structure of kinase domain of DAP kinase with BDB402

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

To be published.

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	278	Homo sapiens	Mutation(s): 0 Gene Names: DAPK1, DAPK 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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P53355
Protein Feature View Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
BD4 Query on BD4 Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A]	B [auth A]	6-(3-AMINOPROPYL)-4,9-DIMETHYLPYRROLO[3,4-C]CARBAZOLE-1,3(2H,6H)-DIONE C₁₉ H₁₉ N₃ O₂ PKPNSCZPIWCHMW-UHFFFAOYSA-N		Ligand Interaction

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.60 Å
R-Value Free: 0.270
R-Value Work: 0.225
R-Value Observed: 0.225
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 77.337	α = 90
b = 108.869	β = 90
c = 50.186	γ = 90

Software Package:

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

Structure Validation

View Full Validation Report

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

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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 R01GM133198.