3LD8 Immune System date Jan 12, 2010
title Structure Of Jmjd6 And Fab Fragments
authors X.Hong, J.Zang, J.White, J.W.Kappler, C.Wang, G.Zhang
compound source
Molecule: Bifunctional Arginine Demethylase And Lysyl-Hydro Jmjd6;
Chain: A
Synonym: Histone Arginine Demethylase Jmjd6, Peptide-Lysine Dioxygenase Jmjd6, Lysyl-Hydroxylase Jmjd6, Jmjc Domain-Con Protein 6, Jumonji Domain-Containing Protein 6, Phosphatidy Receptor, Protein Ptdsr;
Ec: 1.14.11.-
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Jmjd6, Jmjd6(1-403), Kiaa0585, Ptdsr
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Bl21
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet23b

Molecule: Antibody Fab Fragment Light Chain
Chain: B
Engineered: Yes

Organism_scientific: Cricetulus Migratorius
Organism_taxid: 10032
Cell: Hybridoma
Expression_system: Cricetulus Migratorius
Expression_system_taxid: 10032

Molecule: Antibody Fab Fragment Heavy Chain
Chain: C
Engineered: Yes

Organism_scientific: Cricetulus Migratorius
Organism_taxid: 10032
Cell: Hybridoma
Expression_system: Cricetulus Migratorius
Expression_system_taxid: 10032
symmetry Space Group: P 41 21 2
R_factor 0.233 R_Free 0.260
crystal
cell
length a length b length c angle alpha angle beta angle gamma
138.281 138.281 183.554 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.70 Å
ligand FE, GOL, HG, SO4 enzyme Oxidoreductase E.C.1.14.11 BRENDA
Primary referenceInteraction of JMJD6 with single-stranded RNA., Hong X, Zang J, White J, Wang C, Pan CH, Zhao R, Murphy RC, Dai S, Henson P, Kappler JW, Hagman J, Zhang G, Proc Natl Acad Sci U S A. 2010 Aug 17;107(33):14568-72. Epub 2010 Aug 2. PMID:20679243
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (134 Kb) [Save to disk]
  • Biological Unit Coordinates (3ld8.pdb1.gz) 127 Kb
  • LPC: Ligand-Protein Contacts for 3LD8
  • CSU: Contacts of Structural Units for 3LD8
  • Structure Factors (279 Kb)
  • Retrieve 3LD8 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3LD8 from S2C, [Save to disk]
  • Re-refined 3ld8 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3LD8 in 3D
  • Proteopedia, because life has more than 2D.
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  • On FirstGlance, an excellent tool for a guided tour on the structure components, by E. Martz.
  • Visual 3D analysis of 3LD8
  • Cartoon representation from PDB Cartoon
  • 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
  • Crystal Contacts, from CryCo at Weizmann Institute
  • 3D motif for 3LD8, from MSDmotif at EBI
  • Fold representative 3ld8 from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3ld8_A] [3ld8] [3ld8_B] [3ld8_C]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domains found in 3LD8: [IG_like] [IGv] [JmjC ] by SMART
  • Other resources with information on 3LD8
  • Community annotation for 3LD8 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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