2YOB Transferase date Oct 22, 2012
title High Resolution Agxt_m Structure
authors I.Fabelo-Rosa, N.Mesa-Torres, D.Riverol, C.Yunta, A.Albert, E.Sal A.L.Pey
compound source
Molecule: Serine--Pyruvate Aminotransferase
Chain: A, B
Synonym: Spt, Alanine--Glyoxylate Aminotransferase, Agt
Engineered: Yes
Mutation: Yes
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_plasmid: Pcoldii
symmetry Space Group: P 21 21 21
R_factor 0.1695 R_Free 0.2043
length a length b length c angle alpha angle beta angle gamma
54.495 103.525 153.832 90.00 90.00 90.00
method X-Ray Diffractionresolution 1.90 Å
ligand BTB, GOL, PLP, SO4 enzyme
A, B

Primary referenceThe role of protein denaturation energetics and molecular chaperones in the aggregation and mistargeting of mutants causing primary hyperoxaluria type I., Mesa-Torres N, Fabelo-Rosa I, Riverol D, Yunta C, Albert A, Salido E, Pey AL, PLoS One. 2013 Aug 27;8(8):e71963. doi: 10.1371/journal.pone.0071963. PMID:24205397
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (281 Kb) [Save to disk]
  • Biological Unit Coordinates (2yob.pdb1.gz) 276 Kb
  • LPC: Ligand-Protein Contacts for 2YOB
  • CSU: Contacts of Structural Units for 2YOB
  • Structure Factors (510 Kb)
  • Retrieve 2YOB in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 2YOB from S2C, [Save to disk]
  • Re-refined 2yob structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 2YOB 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 2YOB
  • 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 2YOB, from MSDmotif at EBI
  • Fold representative 2yob from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [2yob_B] [2yob_A] [2yob]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 2YOB
  • Community annotation for 2YOB at PDBWiki (http://pdbwiki.org)

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