3P8E Hydrolase Hydrolase Inhibitor date Oct 13, 2010
title Crystal Structure Of Human Dimethylarginine Dimethylaminohyd (Ddah-1) Covalently Bound With N5-(1-Iminopentyl)-L-Ornithi
authors M.Lluis, Y.Wang, A.F.Monzingo, W.Fast, J.D.Robertus
compound source
Molecule: N(G),N(G)-Dimethylarginine Dimethylaminohydrolase
Chain: A, B
Synonym: Ddah-1, Dimethylarginine Dimethylaminohydrolase 1, Dimethylargininase-1;
Ec: 3.5.3.18
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Ddah, Ddah1
Expression_system: Escherichia Coli
Expression_system_taxid: 469008
Expression_system_strain: Bl21(De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet28a-Hddah-1
symmetry Space Group: P 1 21 1
R_factor 0.212 R_Free 0.308
crystal
cell
length a length b length c angle alpha angle beta angle gamma
47.210 80.900 74.090 90.00 90.13 90.00
method X-Ray Diffractionresolution 2.49 Å
ligand LN7 enzyme Hydrolase E.C.3.5.3.18 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A, B


Primary referenceCharacterization of C-Alkyl Amidines as Bioavailable Covalent Reversible Inhibitors of Human DDAH-1., Lluis M, Wang Y, Monzingo AF, Fast W, Robertus JD, ChemMedChem. 2010 Oct 26. PMID:20979083
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (91 Kb) [Save to disk]
  • Biological Unit Coordinates (3p8e.pdb1.gz) 45 Kb
  • Biological Unit Coordinates (3p8e.pdb2.gz) 45 Kb
  • LPC: Ligand-Protein Contacts for 3P8E
  • CSU: Contacts of Structural Units for 3P8E
  • Structure Factors (143 Kb)
  • Retrieve 3P8E in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3P8E from S2C, [Save to disk]
  • Re-refined 3p8e structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3P8E 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 3P8E
  • 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 3P8E, from MSDmotif at EBI
  • Fold representative 3p8e from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3p8e_B] [3p8e] [3p8e_A]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 3P8E
  • Community annotation for 3P8E 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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