3ZHK Immune System date Dec 22, 2012
title The Crystal Structure Of Single Domain Antibody 2x1 Scaffold
authors H.N.Song, E.J.Woo, H.K.Lim
compound source
Molecule: Mg2x1 Scaffold Antibody
Chain: A, B
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Expression_system: Escherichia Coli
Expression_system_taxid: 469008
Expression_system_strain: Bl21(De3)
Expression_system_vector_type: Plasmid
Expression_system_vector: Pet9a
symmetry Space Group: C 1 2 1
R_factor 0.2528 R_Free 0.2977
length a length b length c angle alpha angle beta angle gamma
104.415 55.701 74.539 90.00 126.44 90.00
method X-Ray Diffractionresolution 1.96 Å
ligand SO4 enzyme
A, B

Primary referenceDirected evolution of human heavy chain variable domain (VH) using in vivo protein fitness filter., Kim DS, Song HN, Nam HJ, Kim SG, Park YS, Park JC, Woo EJ, Lim HK, PLoS One. 2014 Jun 3;9(6):e98178. doi: 10.1371/journal.pone.0098178. eCollection , 2014. PMID:24892548
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (41 Kb) [Save to disk]
  • Biological Unit Coordinates (3zhk.pdb1.gz) 37 Kb
  • LPC: Ligand-Protein Contacts for 3ZHK
  • CSU: Contacts of Structural Units for 3ZHK
  • Structure Factors (345 Kb)
  • Retrieve 3ZHK in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3ZHK from S2C, [Save to disk]
  • Re-refined 3zhk structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3ZHK 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 3ZHK
  • Cartoon representation from PDB Cartoon
  • 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
  • Crystal Contacts, from CryCo at Weizmann Institute
  • 3D motif for 3ZHK, from MSDmotif at EBI
  • Fold representative 3zhk from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3zhk_A] [3zhk_B] [3zhk]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domain found in 3ZHK: [IGv ] by SMART
  • Other resources with information on 3ZHK
  • Community annotation for 3ZHK at PDBWiki (http://pdbwiki.org)

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