4L87 Ligase date Jun 16, 2013
title Crystal Structure Of The Human Seryl-Trna Synthetase In Comp Ser-Sa At 2.9 Angstrom Resolution
authors X.Xu, X.L.Yang
compound source
Molecule: Serine--Trna Ligase, Cytoplasmic
Chain: A
Fragment: Unp Residues 2-477
Synonym: Seryl-Trna Synthetase, Serrs, Seryl-Trna(Sersec) Synthetase;
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Sars, Sers
Expression_system: Escherichia Coli
Expression_system_taxid: 469008
Expression_system_strain: Bl21(De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet20b
symmetry Space Group: P 3 2 1
R_factor 0.255 R_Free 0.268
length a length b length c angle alpha angle beta angle gamma
167.074 167.074 65.156 90.00 90.00 120.00
method X-Ray Diffractionresolution 2.90 Å
ligand MG, PO4, SSA enzyme Ligase E.C. BRENDA

Primary referenceCrystal Structure of Human Seryl-tRNA Synthetase and Ser-SA Complex Reveals a Molecular Lever Specific to Higher Eukaryotes., Xu X, Shi Y, Yang XL, Structure. 2013 Oct 1. pii: S0969-2126(13)00342-0. doi:, 10.1016/j.str.2013.08.021. PMID:24095058
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (82 Kb) [Save to disk]
  • Biological Unit Coordinates (4l87.pdb1.gz) 154 Kb
  • LPC: Ligand-Protein Contacts for 4L87
  • CSU: Contacts of Structural Units for 4L87
  • Structure Factors (278 Kb)
  • Retrieve 4L87 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 4L87 from S2C, [Save to disk]
  • Re-refined 4l87 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 4L87 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 4L87
  • 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 4L87, from MSDmotif at EBI
  • Fold representative 4l87 from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [4l87] [4l87_A]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 4L87
  • Community annotation for 4L87 at PDBWiki (http://pdbwiki.org)

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