3DXU	Oxidoreductase	date	Jul 25, 2008
title	The Crystal Structure Of Core Jmjd2d Complexed With Fe And N Oxalylglycine
authors	Z.Chen, G.Zhang
compound		source
Molecule: Jmjc Domain-Containing Histone Demethylation Prot Chain: A Fragment: Unp Residues 8-338 Synonym: Jumonji Domain-Containing Protein 2d Ec: 1.14.11.- Engineered: Yes		Organism_scientific: Homo Sapiens Organism_common: Human Organism_taxid: 9606 Gene: Jmjd2d, Jhdm3d Expression_system: Escherichia Coli Expression_system_taxid: 562 Expression_system_strain: Rossetta De3 Expression_system_vector_type: Plasmid Expression_system_plasmid: Pgext 4t-2
symmetry	Space Group: P 43 21 2	R_factor 0.168 R_Free 0.221
crystal cell	length a length b length c angle alpha angle beta angle gamma 71.543 71.543 150.194 90.00 90.00 90.00
method	X-Ray Diffraction	resolution	2.20 Å
ligand	FE2, GOL, OGA, SO4, ZN	enzyme	Oxidoreductase E.C.1.14.11 BRENDA

Data retrieval

Asymmetric unit, PDB entry: [header only] [complete with coordinates] (69 Kb) [Save to disk] Biological Unit Coordinates (3dxu.pdb1.gz) 61 Kb Biological Unit Coordinates (3dxu.pdb2.gz) 121 Kb LPC: Ligand-Protein Contacts for 3DXU CSU: Contacts of Structural Units for 3DXU Likely Quarternary Molecular Structure file(s) for 3DXU Structure Factors (310 Kb) Retrieve 3DXU in mmCIF format [Save to disk] SEQRES to COORDINATES correlation for 3DXU from S2C, [Save to disk] Re-refined 3dxu structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models

View 3DXU in 3D

Proteopedia, because life has more than 2D. On Jmol, a nice Rasmol like molecule viewer. This is good for easiest viewing of basic structure. On FirstGlance, an excellent tool for a guided tour on the structure components, by E. Martz.

Visual 3D analysis of 3DXU

Ramachandran plot from PDBSum

Structure-derived information

Electron Density related parameters from EDS Electron Density Server, at Upsala Dipole moment, from Dipole Server at Weizmann Institute 3D motif for 3DXU, from MSDmotif at EBI

Sequence-derived information

View one-letter amino acid or nucleotide sequence for each chain: [3dxu] [3dxu_A] SWISS-PROT database: [Q6B0I6] Domain organization of [KDM4D_HUMAN] by SWISSPFAM Domains found in 3DXU: [JmjC] [JmjN ] by SMART

Other resources with information on 3DXU

Community annotation for 3DXU at PDBWiki (http://pdbwiki.org) MMDB (Entrez's Structure Database)

Movements, Movies and Images

Images from IMB Jena Image Library of Biological Macromolecules.

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