3VBB Ligase date Jan 02, 2012
title Crystal Structure Of Seryl-Trna Synthetase From Human At 2.9
authors X.L.Xu, X.L.Yang
compound source
Molecule: Seryl-Trna Synthetase, Cytoplasmic
Chain: A, B, C, D, E, F
Synonym: Serine--Trna Ligase, Serrs, Seryl-Trna(Sersec) Sy
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Sars, Sers
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: E.Coli Bl21(De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet20b
symmetry Space Group: P 21 21 21
R_factor 0.194 R_Free 0.250
length a length b length c angle alpha angle beta angle gamma
116.800 189.417 230.589 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.89 Å
ligand MG, PO4 enzyme Ligase E.C. BRENDA
F, A, D, C, E, B

Primary referenceUnique domain appended to vertebrate tRNA synthetase is essential for vascular development., Xu X, Shi Y, Zhang HM, Swindell EC, Marshall AG, Guo M, Kishi S, Yang XL, Nat Commun. 2012 Feb 21;3:681. doi: 10.1038/ncomms1686. PMID:22353712
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (445 Kb) [Save to disk]
  • Biological Unit Coordinates (3vbb.pdb1.gz) 151 Kb
  • Biological Unit Coordinates (3vbb.pdb2.gz) 150 Kb
  • Biological Unit Coordinates (3vbb.pdb3.gz) 147 Kb
  • LPC: Ligand-Protein Contacts for 3VBB
  • CSU: Contacts of Structural Units for 3VBB
  • Structure Factors (1459 Kb)
  • Retrieve 3VBB in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3VBB from S2C, [Save to disk]
  • Re-refined 3vbb structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3VBB 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 3VBB
  • 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 3VBB, from MSDmotif at EBI
  • Fold representative 3vbb from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3vbb] [3vbb_A] [3vbb_C] [3vbb_D] [3vbb_F] [3vbb_E] [3vbb_B]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 3VBB
  • Community annotation for 3VBB at PDBWiki (http://pdbwiki.org)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

  • You may enter another PDB ID code
    Go [Back], to the [PDB Lite page], to the [OCA Search page] or to the [PDB Home page]
    OCA© by Jaime Prilusky, 1996-2014
    Bioinformatics Unit
    Weizmann Institute of Science