2DEX Hydrolase date Feb 18, 2006
title Crystal Structure Of Human Peptidylarginine Deiminase 4 In C With Histone H3 N-Terminal Peptide Including Arg17
authors K.Arita, T.Shimizu, H.Hashimoto, Y.Hidaka, M.Yamada, M.Sato
compound source
Molecule: Protein-Arginine Deiminase Type Iv
Chain: X
Synonym: Peptidylarginine Deiminase Iv, Hl-60 Pad, Peptidyl Deiminase 4;
Ec: 3.5.3.15
Engineered: Yes
Mutation: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Padi4, Padi5, Pdi5
Expression_system: Escherichia Coli Bl21(De3)
Expression_system_taxid: 469008
Expression_system_strain: Bl21 (De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pgex6p-1

Molecule: 10-Mer Peptide From Histone H3
Chain: A
Engineered: Yes

Synthetic: Yes
Other_details: The Peptide Was Chemically Synthesized.
symmetry Space Group: C 1 2 1
R_factor 0.203 R_Free 0.247
crystal
cell
length a length b length c angle alpha angle beta angle gamma
146.072 60.103 115.703 90.00 124.32 90.00
method X-Ray Diffractionresolution 2.10 Å
ligand CA, SO4 enzyme Hydrolase E.C.3.5.3.15 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
X


Primary referenceStructural basis for histone N-terminal recognition by human peptidylarginine deiminase 4., Arita K, Shimizu T, Hashimoto H, Hidaka Y, Yamada M, Sato M, Proc Natl Acad Sci U S A. 2006 Apr 4;103(14):5291-6. Epub 2006 Mar 27. PMID:16567635
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (110 Kb) [Save to disk]
  • Biological Unit Coordinates (2dex.pdb1.gz) 203 Kb
  • LPC: Ligand-Protein Contacts for 2DEX
  • CSU: Contacts of Structural Units for 2DEX
  • Likely Quarternary Molecular Structure file(s) for 2DEX
  • Structure Factors (369 Kb)
  • Retrieve 2DEX in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 2DEX from S2C, [Save to disk]
  • Re-refined 2dex structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 2DEX 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 2DEX
  • 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 2DEX, from MSDmotif at EBI
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [2dex_X] [2dex_A] [2dex]
  • SWISS-PROT database: [Q9UM07]
  • Domain organization of [PADI4_HUMAN] by SWISSPFAM
  • Other resources with information on 2DEX
  • Community annotation for 2DEX 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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