4PF4 | pdb_00004pf4

1.1A X-RAY STRUCTURE OF THE APO CATALYTIC DOMAIN OF DEATH-ASSOCIATED PROTEIN KINASE 1, aa 1-277

PDB DOI: https://doi.org/10.2210/pdb4PF4/pdb

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

Deposited: 2014-04-28 Released: 2014-05-14
Deposition Author(s): Temmerman, K., Simon, B., Wilmanns, M.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.13 Å
R-Value Free:
0.149 (Depositor), 0.150 (DCC)
R-Value Work:
0.117 (Depositor), 0.120 (DCC)
R-Value Observed:
0.118 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

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

Literature

1.1A X-RAY STRUCTURE OF THE APO CATALYTIC DOMAIN OF DEATH-ASSOCIATED PROTEIN KINASE 1, aa 1-277

Temmerman, K., Simon, B., Wilmanns, M.

To be published.

Macromolecule Content

Total Structure Weight: 33 kDa
Atom Count: 2,909
Modeled Residue Count: 278
Deposited Residue Count: 278
Unique protein chains: 1

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: 2.7.11.1
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 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain B [auth A] SDF format, chain C [auth A] SDF format, chain D [auth A] SDF format, chain E [auth A] MOL2 format, chain B [auth A] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] mmCIF format, chain B [auth A] mmCIF format, chain C [auth A] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A]	B [auth A], C [auth A], D [auth A], E [auth A]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain B [auth A] Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Interactions & Density Focus chain B [auth A] Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain K [auth A] SDF format, chain L [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] MOL2 format, chain L [auth A] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain J [auth A] mmCIF format, chain K [auth A] mmCIF format, chain L [auth A]	G [auth A] H [auth A] I [auth A] J [auth A] K [auth A] G [auth A], H [auth A], I [auth A], J [auth A], K [auth A], L [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Interactions & Density Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain N [auth A] MOL2 format, chain N [auth A] mmCIF format, chain N [auth A]	N [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain N [auth A] Interactions & Density Focus chain N [auth A]
NA Query on NA Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain M [auth A] MOL2 format, chain F [auth A] MOL2 format, chain M [auth A] mmCIF format, chain F [auth A] mmCIF format, chain M [auth A]	F [auth A], M [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain M [auth A] Interactions & Density Focus chain F [auth A] Focus chain M [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.13 Å
R-Value Free: 0.149 (Depositor), 0.150 (DCC)
R-Value Work: 0.117 (Depositor), 0.120 (DCC)
R-Value Observed: 0.118 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 46.516	α = 90
b = 62.005	β = 90
c = 88.375	γ = 90

Software Package:

Software Name	Purpose
SCALA	data scaling
MOLREP	phasing
PDB_EXTRACT	data extraction
REFMAC	refinement
XDS	data reduction
XSCALE	data reduction

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2014-05-14

Deposition Author(s):

Temmerman, K.

Simon, B.

Wilmanns, M.

Revision History (Full details and data files)

Version 1.0: 2014-05-14
Type: Initial release
Version 1.1: 2014-07-16
Changes: Database references, Structure summary
Version 1.2: 2023-12-20
Changes: Data collection, Database references, Derived calculations, Refinement description