4E4H | pdb_00004e4h

Crystal structure of Histone Demethylase NO66

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.28 Å
  • R-Value Free: 
    0.252 (Depositor), 0.261 (DCC) 
  • R-Value Work: 
    0.202 (Depositor) 
  • R-Value Observed: 
    0.204 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 4E4H

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

Literature

tructural Basis for Tetramerization-dependent Gene Repression by Histone Demethylase NO66

Tao, Y., Wu, M., Sinha, K.M., Zang, J.

To be published.

Macromolecule Content 

  • Total Structure Weight: 211.11 kDa 
  • Atom Count: 15,448 
  • Modeled Residue Count: 1,825 
  • Deposited Residue Count: 1,852 
  • Unique protein chains: 1

Macromolecules

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|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Lysine-specific demethylase NO66
A, B, C, D
463Homo sapiensMutation(s): 0 
Gene Names: C14orf169, NO66
EC: 1.14.11.27 (PDB Primary Data), 1.14.11.79 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for Q9H6W3 (Homo sapiens)
Explore Q9H6W3 
Go to UniProtKB:  Q9H6W3
PHAROS:  Q9H6W3
GTEx:  ENSG00000170468 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9H6W3
Sequence Annotations
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Reference Sequence

Small Molecules

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

Query on PEG


Download:Ideal Coordinates CCD File
J [auth C]DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
GOL

Query on GOL


Download:Ideal Coordinates CCD File
I [auth C]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
ACT

Query on ACT


Download:Ideal Coordinates CCD File
F [auth A]ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
FE

Query on FE


Download:Ideal Coordinates CCD File
E [auth A],
G [auth B],
H [auth C],
K [auth D]		FE (III) ION
Fe
VTLYFUHAOXGGBS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.28 Å
  • R-Value Free:  0.252 (Depositor), 0.261 (DCC) 
  • R-Value Work:  0.202 (Depositor) 
  • R-Value Observed: 0.204 (Depositor) 
Space Group: P 32
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 89.352α = 90
b = 89.352β = 90
c = 304.863γ = 120
Software Package:
Software NamePurpose
ADSCdata collection
PHASERphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report



View more in-depth experimental data

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-01-30
    Type: Initial release
  • Version 1.1: 2024-03-20
    Changes: Data collection, Database references, Derived calculations
  • Version 1.2: 2024-04-03
    Changes: Refinement description