3NVX Viral Protein date Jul 08, 2010
title Molecular Mechanism Of Guidance Cue Recognition
authors H.Liu, Z.Juo, A.Shim, P.Focia, X.Chen, C.Garcia, X.He
compound source
Molecule: Protein A39
Chain: A, B
Fragment: Unp Residues 15-396
Engineered: Yes
Organism_scientific: Vaccinia Virus
Organism_taxid: 10249
Strain: Copenhagen
Gene: A39r
Expression_system: Spodoptera Frugiperda
Expression_system_taxid: 7108
Expression_system_strain: Hi5
symmetry Space Group: C 2 2 21
R_factor 0.176 R_Free 0.225
length a length b length c angle alpha angle beta angle gamma
51.088 171.006 211.175 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.00 Å
ligand NAG enzyme
A, B

Primary referenceStructural basis of semaphorin-plexin recognition and viral mimicry from Sema7A and A39R complexes with PlexinC1., Liu H, Juo ZS, Shim AH, Focia PJ, Chen X, Garcia KC, He X, Cell. 2010 Sep 3;142(5):749-61. Epub 2010 Aug 19. PMID:20727575
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (142 Kb) [Save to disk]
  • Biological Unit Coordinates (3nvx.pdb1.gz) 71 Kb
  • Biological Unit Coordinates (3nvx.pdb2.gz) 68 Kb
  • LPC: Ligand-Protein Contacts for 3NVX
  • CSU: Contacts of Structural Units for 3NVX
  • Structure Factors (502 Kb)
  • Retrieve 3NVX in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3NVX from S2C, [Save to disk]
  • Re-refined 3nvx structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3NVX 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 3NVX
  • 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 3NVX, from MSDmotif at EBI
  • Fold representative 3nvx from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3nvx_B] [3nvx] [3nvx_A]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domain found in 3NVX: [Sema ] by SMART
  • Other resources with information on 3NVX
  • Community annotation for 3NVX 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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