6E7O Lipid Binding Protein date Jul 27, 2018
title Crystal Structure Of Deglycosylated Human Epdr1
authors Y.Wei, G.G.Prive
compound source
Molecule: Mammalian Ependymin-Related Protein 1
Chain: A, B, C, D
Synonym: Merp-1,Upregulated In Colorectal Cancer Gene 1 Pro
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Epdr1, Merp1, Ucc1
Expression_system: Homo Sapiens
Expression_system_taxid: 9606
Expression_system_cell_line: Hek293s Gnti-
Expression_system_atcc_number: Crl-3022
Expression_system_plasmid: Pb-T-Paf
symmetry Space Group: C 2 2 21
R_factor 0.255 R_Free 0.278
crystal
cell
length a length b length c angle alpha angle beta angle gamma
87.805 97.482 189.469 90.00 90.00 90.00
method X-Ray Diffractionresolution 3.00 Å
Gene
Ontology
ChainFunctionProcessComponent
A, D, C, B


Primary referenceCrystal structures of human lysosomal EPDR1 reveal homology with the superfamily of bacterial lipoprotein transporters., Wei Y, Xiong ZJ, Li J, Zou C, Cairo CW, Klassen JS, Prive GG, Commun Biol. 2019 Feb 5;2:52. doi: 10.1038/s42003-018-0262-9. eCollection 2019. PMID:30729188
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (223 Kb) [Save to disk]
  • Biological Unit Coordinates (6e7o.pdb1.gz) 113 Kb
  • Biological Unit Coordinates (6e7o.pdb2.gz) 106 Kb
  • CSU: Contacts of Structural Units for 6E7O
  • Structure Factors (311 Kb)
  • Retrieve 6E7O in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 6E7O from S2C, [Save to disk]
  • View 6E7O 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 6E7O
  • Cartoon representation from PDB Cartoon
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
  • Crystal Contacts, from CryCo at Weizmann Institute
  • Fold representative 6e7o from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [6e7o_B] [6e7o_C] [6e7o_A] [6e7o_D]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 6E7O
  • Community annotation for 6E7O at PDBWiki (http://pdbwiki.org)

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