5GRQ

Crystal Structure of DHB domain of Daxx in complex with an ATRX peptide

PDB DOI: https://doi.org/10.2210/pdb5GRQ/pdb

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

Deposited: 2016-08-12 Released: 2017-09-27
Deposition Author(s): Li, H.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.58 Å
R-Value Free: 0.179
R-Value Work: 0.158
R-Value Observed: 0.159

wwPDB Validation 3D Report Full Report

This is version 2.1 of the entry. See complete history.

Literature

Crystal Structure of DHB domain of Daxx in complex with an ATRX peptide

Li, H.

To be published.

Macromolecule Content

Total Structure Weight: 29.16 kDa
Atom Count: 2,331
Modelled Residue Count: 231
Deposited Residue Count: 240
Unique protein chains: 2

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Death domain-associated protein 6	A, B	90	Homo sapiens	Mutation(s): 0 Gene Names: DAXX, BING2, DAP6
UniProt & NIH Common Fund Data Resources
Find proteins for Q9UER7 (Homo sapiens) Explore Q9UER7 Go to UniProtKB: Q9UER7
PHAROS: Q9UER7 GTEx: ENSG00000204209
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9UER7
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Transcriptional regulator ATRX	C, D	30	Homo sapiens	Mutation(s): 0 Gene Names: ATRX, RAD54L, XH2 EC: 3.6.4.12
UniProt & NIH Common Fund Data Resources
Find proteins for P46100 (Homo sapiens) Explore P46100 Go to UniProtKB: P46100
PHAROS: P46100 GTEx: ENSG00000085224
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P46100
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain G [auth A] MOL2 format, chain G [auth A]	G [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Interactions & Density Focus chain G [auth A]
ZN Query on ZN Download Ideal Coordinates CCD File SDF format, chain K [auth A] SDF format, chain L [auth A] SDF format, chain M [auth A] SDF format, chain P [auth A] SDF format, chain Q [auth A] SDF format, chain R [auth A] SDF format, chain T [auth B] SDF format, chain U [auth B] SDF format, chain W [auth C] SDF format, chain X [auth C] SDF format, chain Y [auth C] MOL2 format, chain K [auth A] MOL2 format, chain L [auth A] MOL2 format, chain M [auth A] MOL2 format, chain P [auth A] MOL2 format, chain Q [auth A] MOL2 format, chain R [auth A] MOL2 format, chain T [auth B] MOL2 format, chain U [auth B] MOL2 format, chain W [auth C] MOL2 format, chain X [auth C] MOL2 format, chain Y [auth C]	K [auth A] L [auth A] M [auth A] P [auth A] Q [auth A] K [auth A], L [auth A], M [auth A], P [auth A], Q [auth A], R [auth A], T [auth B], U [auth B], W [auth C], X [auth C], Y [auth C]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain P [auth A] Focus chain Q [auth A] Focus chain R [auth A] Focus chain T [auth B] Focus chain U [auth B] Focus chain W [auth C] Focus chain X [auth C] Focus chain Y [auth C] Interactions & Density Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain P [auth A] Focus chain Q [auth A] Focus chain R [auth A] Focus chain T [auth B] Focus chain U [auth B] Focus chain W [auth C] Focus chain X [auth C] Focus chain Y [auth C]
ACT Query on ACT Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain N [auth A] SDF format, chain O [auth A] SDF format, chain V [auth C] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain N [auth A] MOL2 format, chain O [auth A] MOL2 format, chain V [auth C]	E [auth A], F [auth A], N [auth A], O [auth A], V [auth C]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain N [auth A] Focus chain O [auth A] Focus chain V [auth C] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain N [auth A] Focus chain O [auth A] Focus chain V [auth C]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain S [auth B] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain S [auth B]	H [auth A], I [auth A], J [auth A], S [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain S [auth B] Interactions & Density Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain S [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.58 Å
R-Value Free: 0.179
R-Value Work: 0.158
R-Value Observed: 0.159
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 53.428	α = 90
b = 56.217	β = 90
c = 102.917	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
SCALEPACK	data scaling
PDB_EXTRACT	data extraction
HKL-3000	data reduction
SHELXDE	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 2017-09-27

Deposition Author(s):

Li, H.

Revision History (Full details and data files)

Version 1.0: 2017-09-27
Type: Initial release
Version 2.0: 2017-10-18
Changes: Advisory, Atomic model, Database references, Polymer sequence, Source and taxonomy, Structure summary
Version 2.1: 2024-03-20
Changes: Data collection, Database references, Derived calculations