3ZXT | pdb_00003zxt

Dimeric structure of DAPK-1 catalytic domain in complex with AMPPCP- Mg

PDB DOI: https://doi.org/10.2210/pdb3ZXT/pdb

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

Deposited: 2011-08-15 Released: 2012-07-25
Deposition Author(s): de Diego, I., Lehmann, F., Wilmanns, M.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.65 Å
R-Value Free:
0.285 (Depositor), 0.284 (DCC)
R-Value Work:
0.216 (Depositor), 0.216 (DCC)
R-Value Observed:
0.219 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

A Journey Through the Dap Kinase Architecture

De Diego, I., Kuper, J., Lehmann, F., Wilmanns, M.

To be published.

Macromolecule Content

Total Structure Weight: 133.07 kDa
Atom Count: 7,932
Modeled Residue Count: 1,006
Deposited Residue Count: 1,140
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DEATH-ASSOCIATED PROTEIN KINASE 1	A, B, C, D	285	Homo sapiens	Mutation(s): 0 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
ACP Query on ACP Download:Ideal Coordinates CCD File SDF format, chain J [auth B] SDF format, chain L [auth C] SDF format, chain M [auth D] SDF format, chain E [auth A] MOL2 format, chain J [auth B] MOL2 format, chain L [auth C] MOL2 format, chain M [auth D] MOL2 format, chain E [auth A] mmCIF format, chain J [auth B] mmCIF format, chain L [auth C] mmCIF format, chain M [auth D] mmCIF format, chain E [auth A]	E [auth A], J [auth B], L [auth C], M [auth D]	PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER C₁₁ H₁₈ N₅ O₁₂ P₃ UFZTZBNSLXELAL-IOSLPCCCSA-N		Interactions Focus chain E [auth A] Focus chain J [auth B] Focus chain L [auth C] Focus chain M [auth D] Interactions & Density Focus chain E [auth A] Focus chain J [auth B] Focus chain L [auth C] Focus chain M [auth D]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain N [auth D] SDF format, chain K [auth C] SDF format, chain I [auth B] SDF format, chain H [auth B] SDF format, chain G [auth A] SDF format, chain F [auth A] MOL2 format, chain N [auth D] MOL2 format, chain K [auth C] MOL2 format, chain I [auth B] MOL2 format, chain H [auth B] MOL2 format, chain G [auth A] MOL2 format, chain F [auth A] mmCIF format, chain N [auth D] mmCIF format, chain K [auth C] mmCIF format, chain I [auth B] mmCIF format, chain H [auth B] mmCIF format, chain G [auth A] mmCIF format, chain F [auth A]	F [auth A] G [auth A] H [auth B] I [auth B] K [auth C] F [auth A], G [auth A], H [auth B], I [auth B], K [auth C], N [auth D]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth B] Focus chain I [auth B] Focus chain K [auth C] Focus chain N [auth D] Interactions & Density Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth B] Focus chain I [auth B] Focus chain K [auth C] Focus chain N [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.65 Å
R-Value Free: 0.285 (Depositor), 0.284 (DCC)
R-Value Work: 0.216 (Depositor), 0.216 (DCC)
R-Value Observed: 0.219 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 83.407	α = 90
b = 76.578	β = 92.01
c = 106.892	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2012-07-25

Deposition Author(s):

de Diego, I.

Lehmann, F.

Wilmanns, M.

Revision History (Full details and data files)

Version 1.0: 2012-07-25
Type: Initial release
Version 1.1: 2023-12-20
Changes: Data collection, Database references, Derived calculations, Other, Refinement description

3ZXT | pdb_00003zxt

Dimeric structure of DAPK-1 catalytic domain in complex with AMPPCP- Mg

Literature

A Journey Through the Dap Kinase Architecture

Biological Assembly 1

Biological Assembly 2

Macromolecules

Entity ID: 1

UniProt & NIH Common Fund Data Resources

Entity Groups

Sequence Annotations

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