4L7E

Three dimensional structure of mutant D78A of human HD domain-containing protein 2, Genomics Consortium (NESG) Target HR6723


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.229 Å
  • R-Value Free: 0.215 
  • R-Value Work: 0.174 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history


Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
HD domain-containing protein 2
A, B
204Homo sapiensMutation(s): 1 
Gene Names: HDDC2 (C6orf74, NS5ATP2)
Find proteins for Q7Z4H3 (Homo sapiens)
Go to Gene View: HDDC2
Go to UniProtKB:  Q7Z4H3
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CL
Query on CL

Download SDF File 
Download CCD File 
A, B
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
PEG
Query on PEG

Download SDF File 
Download CCD File 
A, B
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  2 Unique
IDChainsTypeFormula2D DiagramParent
SEP
Query on SEP
A, B
L-PEPTIDE LINKINGC3 H8 N O6 PSER
MSE
Query on MSE
A, B
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.229 Å
  • R-Value Free: 0.215 
  • R-Value Work: 0.174 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 65.762α = 90.00
b = 68.886β = 90.00
c = 106.154γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
BALBESphasing
HKL-2000data scaling
ADSCdata collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Revision History 

  • Version 1.0: 2013-07-24
    Type: Initial release
  • Version 1.1: 2018-01-24
    Type: Database references, Structure summary