3WNX Protein Transport date Dec 18, 2013
title Crystal Structure Of Ergic-53mcfd2, Calciumman3-Bound Form
authors T.Satoh, K.Suzuki, T.Yamaguchi, K.Kato
compound source
Molecule: Protein Ergic-53
Chain: A
Fragment: Carbohydrate Recognition Domain (Unp Residues 31-
Synonym: Er-Golgi Intermediate Compartment 53 Kda Protein, Intracellular Mannose-Specific Lectin Mr60, Lectin Mannose-
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Ergic53
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Bl21-Codonplus(De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pcold-III

Molecule: Multiple Coagulation Factor Deficiency Protein 2
Chain: B
Fragment: Unp Residues 67-146
Synonym: Mcfd2, Neural Stem Cell-Derived Neuronal Survival
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Mcfd2
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Bl21-Codonplus(De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet-16b
symmetry Space Group: C 1 2 1
R_factor 0.203 R_Free 0.287
crystal
cell
length a length b length c angle alpha angle beta angle gamma
100.257 58.212 55.435 90.00 109.32 90.00
method X-Ray Diffractionresolution 2.75 Å
ligand CA, MAN enzyme
Gene
Ontology
ChainFunctionProcessComponent
A


B


Primary referenceStructural Basis for Disparate Sugar-Binding Specificities in the Homologous Cargo Receptors ERGIC-53 and VIP36., Satoh T, Suzuki K, Yamaguchi T, Kato K, PLoS One. 2014 Feb 3;9(2):e87963. doi: 10.1371/journal.pone.0087963. eCollection , 2014. PMID:24498414
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (52 Kb) [Save to disk]
  • Biological Unit Coordinates (3wnx.pdb1.gz) 46 Kb
  • LPC: Ligand-Protein Contacts for 3WNX
  • CSU: Contacts of Structural Units for 3WNX
  • Structure Factors (154 Kb)
  • Retrieve 3WNX in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3WNX from S2C, [Save to disk]
  • Re-refined 3wnx structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3WNX 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 3WNX
  • 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
  • 3D motif for 3WNX, from MSDmotif at EBI
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3wnx_B] [3wnx_A] [3wnx]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 3WNX
  • Community annotation for 3WNX at PDBWiki (http://pdbwiki.org)

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