5GRQ | pdb_00005grq

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

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.58 Å
  • R-Value Free: 
    0.179 (Depositor), 0.182 (DCC) 
  • R-Value Work: 
    0.158 (Depositor), 0.162 (DCC) 
  • R-Value Observed: 
    0.159 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 5GRQ

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 
  • Modeled Residue Count: 231 
  • Deposited Residue Count: 240 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:
|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Death domain-associated protein 6
A, B
90Homo sapiensMutation(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 Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9UER7
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:
|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Transcriptional regulator ATRX
C, D
30Homo sapiensMutation(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 Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP46100
Sequence Annotations
Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
GOL

Query on GOL


Download:Ideal Coordinates CCD File
G [auth A]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
ZN

Query on ZN


Download:Ideal Coordinates CCD File
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
ACT

Query on ACT


Download:Ideal Coordinates CCD File
E [auth A],
F [auth A],
N [auth A],
O [auth A],
V [auth C]		ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
CL

Query on CL


Download:Ideal Coordinates CCD File
H [auth A],
I [auth A],
J [auth A],
S [auth B]		CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.58 Å
  • R-Value Free:  0.179 (Depositor), 0.182 (DCC) 
  • R-Value Work:  0.158 (Depositor), 0.162 (DCC) 
  • R-Value Observed: 0.159 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 53.428α = 90
b = 56.217β = 90
c = 102.917γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
SCALEPACKdata scaling
PDB_EXTRACTdata extraction
HKL-3000data reduction
SHELXDEphasing

Structure Validation

View Full Validation Report



View more in-depth experimental data

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