3ZHD Immune System date Dec 21, 2012
title The Crystal Structure Of Single Domain Antibody 8-4 Scaffold.
authors H.N.Song, E.J.Woo, H.K.Lim
compound source
Molecule: Mg8-4 Scaffold Antibody
Chain: A, B
Engineered: Yes
Other_details: Human Heavy Chain Domain
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: P 3 2 1
R_factor 0.1779 R_Free 0.2311
length a length b length c angle alpha angle beta angle gamma
87.079 87.079 55.738 90.00 90.00 120.00
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] (46 Kb) [Save to disk]
  • Biological Unit Coordinates (3zhd.pdb1.gz) 123 Kb
  • LPC: Ligand-Protein Contacts for 3ZHD
  • CSU: Contacts of Structural Units for 3ZHD
  • Structure Factors (243 Kb)
  • Retrieve 3ZHD in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3ZHD from S2C, [Save to disk]
  • Re-refined 3zhd structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3ZHD 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 3ZHD
  • 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 3ZHD, from MSDmotif at EBI
  • Fold representative 3zhd from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3zhd_A] [3zhd_B] [3zhd]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domain found in 3ZHD: [IGv ] by SMART
  • Other resources with information on 3ZHD
  • Community annotation for 3ZHD at PDBWiki (http://pdbwiki.org)

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