3U4S | pdb_00003u4s

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

• PDB DOI: https://doi.org/10.2210/pdb3U4S/pdb

• Classification: OXIDOREDUCTASE/OXIDOREDUCTASE SUBSTRATE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2011-10-10 Released: 2012-02-08 
• Deposition Author(s): Ma, J., McDonough, M.A., Schofield, C.J.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.15 Å
• R-Value Free: 
  0.222 (Depositor), 0.218 (DCC) 
• R-Value Work: 
  0.181 (Depositor), 0.177 (DCC) 
• R-Value Observed: 
  0.183 (Depositor) 

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

• PubMed: 22241642 
• DOI: https://doi.org/10.1002/anie.201107833
• Primary Citation Related Structures: 
  3U4S

---

Organizational Affiliation: 
• Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road, Oxford, OX1 3TA, UK.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 90.99 kDa 
• Atom Count: 6,189 
• Modeled Residue Count: 708 
• Deposited Residue Count: 778 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Lysine-specific demethylase 4A	A, B	381	Homo sapiens	Mutation(s): 0  Gene Names: JHDM3A, JMJD2, JMJD2A, KDM4A, KIAA0677 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 ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
HISTONE 3 TAIL ANALOG (T11C Peptide)	C, D	8	N/A	Mutation(s): 1
UniProt & NIH Common Fund Data Resources
Find proteins for P68431 (Homo sapiens) Explore P68431  Go to UniProtKB:  P68431
PHAROS:  P68431 GTEx:  ENSG00000197409 ENSG00000197153 ENSG00000278828 ENSG00000275714 ENSG00000273983 ENSG00000274750 ENSG00000275379 ENSG00000277775

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
08P	G [auth A], J [auth B]	N-(carboxycarbonyl)-D-cysteine C5 H7 N O5 S JOFZGZRXVKSFKN-UWTATZPHSA-N
ZN	F [auth A], I [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
NI	E [auth A], H [auth B]	NICKEL (II) ION Ni VEQPNABPJHWNSG-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
M3L	C, D	L-PEPTIDE LINKING	C9 H21 N2 O2		LYS

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.15 Å
• R-Value Free:  0.222 (Depositor), 0.218 (DCC) 
• R-Value Work:  0.181 (Depositor), 0.177 (DCC) 
• R-Value Observed: 0.183 (Depositor) 

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 99.819	α = 90
b = 150.06	β = 90
c = 55.917	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
PHASER	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction
GDA	data collection

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-02-08 
Deposition Author(s): Ma, J., McDonough, M.A., Schofield, C.J.

Revision History  

• Version 1.0: 2012-02-08
  Type: Initial release
  
• Version 1.1: 2012-02-22
  Changes: Database references
• Version 1.2: 2024-02-28
  Changes: Data collection, Database references, Derived calculations