3U4S

Histone Lysine demethylase JMJD2A in complex with T11C peptide substrate crosslinked to N-oxalyl-D-cysteine


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free: 0.222 
  • R-Value Work: 0.181 
  • R-Value Observed: 0.183 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Linking of 2-Oxoglutarate and Substrate Binding Sites Enables Potent and Highly Selective Inhibition of JmjC Histone Demethylases.

Woon, E.C.Tumber, A.Kawamura, A.Hillringhaus, L.Ge, W.Rose, N.R.Ma, J.H.Chan, M.C.Walport, L.J.Che, K.H.Ng, S.S.Marsden, B.D.Oppermann, U.McDonough, M.A.Schofield, C.J.

(2012) Angew Chem Int Ed Engl 51: 1631-1634


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Lysine-specific demethylase 4AA, B381Homo sapiensMutation(s): 0 
Gene Names: JHDM3AJMJD2JMJD2AKDM4AKIAA0677
EC: 1.14.11 (PDB Primary Data), 1.14.11.66 (UniProt), 1.14.11.69 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for O75164 (Homo sapiens)
Explore O75164 
Go to UniProtKB:  O75164
PHAROS:  O75164
GTEx:  ENSG00000066135 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO75164
Protein Feature View
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  • Reference Sequence

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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
HISTONE 3 TAIL ANALOG (T11C Peptide)C, D8N/AMutation(s): 1 
UniProt & NIH Common Fund Data Resources
Find proteins for P68431 (Homo sapiens)
Explore P68431 
Go to UniProtKB:  P68431
PHAROS:  P68431
Entity Groups  
UniProt GroupP68431
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
08P
Query on 08P

Download Ideal Coordinates CCD File 
G [auth A],
J [auth B]
N-(carboxycarbonyl)-D-cysteine
C5 H7 N O5 S
JOFZGZRXVKSFKN-UWTATZPHSA-N
 Ligand Interaction
ZN
Query on ZN

Download Ideal Coordinates CCD File 
F [auth A],
I [auth B]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
NI
Query on NI

Download Ideal Coordinates CCD File 
E [auth A],
H [auth B]
NICKEL (II) ION
Ni
VEQPNABPJHWNSG-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
M3L
Query on M3L
C, D L-PEPTIDE LINKINGC9 H21 N2 O2LYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free: 0.222 
  • R-Value Work: 0.181 
  • R-Value Observed: 0.183 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 99.819α = 90
b = 150.06β = 90
c = 55.917γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACTdata extraction
GDAdata collection

Structure Validation

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Ligand Structure Quality Assessment 



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-02-08
    Type: Initial release
  • Version 1.1: 2012-02-22
    Changes: Database references