6DK1 Membrane Protein date May 28, 2018
title Human Sigma-1 Receptor Bound To (+)-Pentazocine
authors H.R.Schmidt, A.C.Kruse
compound source
Molecule: Sigma Non-Opioid Intracellular Receptor 1
Chain: A, B, C
Synonym: Aging-Associated Gene 8 Protein,Sr31747-Binding Pr Bp,Sigma 1-Type Opioid Receptor,Hsigmar1;
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Sigmar1, Oprs1, Srbp, Aag8
Expression_system: Spodoptera Frugiperda
Expression_system_common: Fall Armyworm
Expression_system_taxid: 7108
symmetry Space Group: P 21 21 2
R_factor 0.247 R_Free 0.278
crystal
cell
length a length b length c angle alpha angle beta angle gamma
84.837 128.590 109.180 90.00 90.00 90.00
method X-Ray Diffractionresolution 3.12 Å
ligand GM4, GOL, OLC, SO4 enzyme
Gene
Ontology
ChainFunctionProcessComponent
A, C, B
  • opioid receptor activity


  • Primary referenceStructural basis for sigma1 receptor ligand recognition., Schmidt HR, Betz RM, Dror RO, Kruse AC, Nat Struct Mol Biol. 2018 Oct;25(10):981-987. doi: 10.1038/s41594-018-0137-2., Epub 2018 Oct 5. PMID:30291362
    Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (117 Kb) [Save to disk]
  • Biological Unit Coordinates (6dk1.pdb1.gz) 109 Kb
  • LPC: Ligand-Protein Contacts for 6DK1
  • CSU: Contacts of Structural Units for 6DK1
  • Structure Factors (521 Kb)
  • Retrieve 6DK1 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 6DK1 from S2C, [Save to disk]
  • View 6DK1 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 6DK1
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1h6dk1, region K:52-212,K:375-433 [Jmol] [rasmolscript] [script source]
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [6dk1_C] [6dk1_B] [6dk1_A]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 6DK1
  • Community annotation for 6DK1 at PDBWiki (http://pdbwiki.org)

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