6VGO Hydrolase date Jan 08, 2020
title Crystal Structure Of Human Dipeptidase 3
authors K.Hayashi, K.L.Longenecker, S.Vivona
compound source
Molecule: Dipeptidase 3
Chain: A
Ec: 3.4.13.19
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Dpep3, Unq834pro1772
Expression_system: Cricetulus Griseus
Expression_system_common: Chinese Hamster
Expression_system_taxid: 10029
symmetry Space Group: P 43 21 2
R_factor 0.186 R_Free 0.214
crystal
cell
length a length b length c angle alpha angle beta angle gamma
65.880 65.880 194.310 90.00 90.00 90.00
method X-Ray Diffractionresolution 1.82 Å
ligand
enzyme Hydrolase E.C.3.4.13.19 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A


Primary referenceStructure of human DPEP3 in complex with the SC-003 antibody Fab fragment reveals basis for lack of dipeptidase activity., Hayashi K, Longenecker KL, Koenig P, Prashar A, Hampl J, Stoll V, Vivona S, J Struct Biol. 2020 Apr 20:107512. doi: 10.1016/j.jsb.2020.107512. PMID:32325220
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (64 Kb) [Save to disk]
  • Biological Unit Coordinates (6vgo.pdb1.gz) 116 Kb
  • CSU: Contacts of Structural Units for 6VGO
  • Structure Factors (1573 Kb)
  • Retrieve 6VGO in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 6VGO from S2C, [Save to disk]
  • View 6VGO 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 6VGO
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [6vgo_A]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 6VGO
  • Community annotation for 6VGO at PDBWiki (http://pdbwiki.org)

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