5E33 Hydrolase date Oct 01, 2015
title Structure Of Human Dpp3 In Complex With Met-Enkephalin
authors P.Kumar, V.Reithofer, M.Reisinger, T.Pavkov-Keller, S.Wallner, P.Macheroux, K.Gruber
compound source
Molecule: Dipeptidyl Peptidase 3
Chain: A
Synonym: Dipeptidyl Aminopeptidase III,Dipeptidyl Arylamida Dipeptidyl Peptidase III,Dpp III,Enkephalinase B;
Ec: 3.4.14.4
Engineered: Yes
Mutation: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Dpp3
Expression_system: Escherichia Coli Bl21(De3)
Expression_system_common: Human
Expression_system_taxid: 469008
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet28mhl

Molecule: Met-Enkephalin
Chain: B
Engineered: Yes

Synthetic: Yes
Organism_scientific: Homo Sapiens
Organism_taxid: 9606
symmetry Space Group: C 1 2 1
R_factor 0.182 R_Free 0.224
crystal
cell
length a length b length c angle alpha angle beta angle gamma
119.790 105.760 65.167 90.00 93.49 90.00
method X-Ray Diffractionresolution 1.84 Å
ligand K, MG, ZN enzyme Hydrolase E.C.3.4.14.4 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A


Primary referenceSubstrate complexes of human dipeptidyl peptidase III reveal the mechanism of enzyme inhibition., Kumar P, Reithofer V, Reisinger M, Wallner S, Pavkov-Keller T, Macheroux P, Gruber K, Sci Rep. 2016 Mar 30;6:23787. doi: 10.1038/srep23787. PMID:27025154
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (133 Kb) [Save to disk]
  • Biological Unit Coordinates (5e33.pdb1.gz) 127 Kb
  • LPC: Ligand-Protein Contacts for 5E33
  • CSU: Contacts of Structural Units for 5E33
  • Structure Factors (568 Kb)
  • Retrieve 5E33 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5E33 from S2C, [Save to disk]
  • Re-refined 5e33 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 5E33 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 5E33
  • 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
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [5e33] [5e33_B] [5e33_A]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 5E33
  • Community annotation for 5E33 at PDBWiki (http://pdbwiki.org)

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