1Z9M Cell Adhesion date Apr 03, 2005
title Crystal Structure Of Nectin-Like Molecule-1 Protein Domain 1
authors X.Dong, F.Xu, Y.Gong, J.Gao, P.Lin, T.Chen, Y.Peng, B.Qiang, J.Yuan, X.Peng, Z.Rao
compound source
Molecule: Gapa225
Chain: A, B
Fragment: Residues 37-141
Synonym: Nectin-Like Molecule_1 Domain 1
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Expression_system: Escherichia Coli Bl21
Expression_system_taxid: 511693
Expression_system_strain: Bl21
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet32a
symmetry Space Group: C 2 2 21
R_factor 0.227 R_Free 0.274
crystal
cell
length a length b length c angle alpha angle beta angle gamma
77.100 77.500 102.200 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.40 Å
note 1Z9M is a representative structure
Primary referenceCrystal Structure of the V Domain of Human Nectin-like Molecule-1/Syncam3/Tsll1/Igsf4b, a Neural Tissue-specific Immunoglobulin-like Cell-Cell Adhesion Molecule., Dong X, Xu F, Gong Y, Gao J, Lin P, Chen T, Peng Y, Qiang B, Yuan J, Peng X, Rao Z, J Biol Chem. 2006 Apr 14;281(15):10610-7. Epub 2006 Feb 7. PMID:16467305
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (42 Kb) [Save to disk]
  • Biological Unit Coordinates (1z9m.pdb1.gz) 37 Kb
  • CSU: Contacts of Structural Units for 1Z9M
  • Likely Quarternary Molecular Structure file(s) for 1Z9M
  • Structure Factors (320 Kb)
  • Retrieve 1Z9M in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1Z9M from S2C, [Save to disk]
  • Re-refined 1z9m structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 1Z9M 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 1Z9M
  • 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 1Z9M, from MSDmotif at EBI
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [1z9m_B] [1z9m] [1z9m_A]
  • SWISS-PROT database: [Q8N126]
  • Domain organization of [CADM3_HUMAN] by SWISSPFAM
  • Domains found in 1Z9M: [IG] [RNAse_Pc ] by SMART
  • Other resources with information on 1Z9M
  • Community annotation for 1Z9M at PDBWiki (http://pdbwiki.org)
  • MMDB (Entrez's Structure Database)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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