3R9A Transferase Transport Protein date Mar 25, 2011
title Human Alanine-Glyoxylate Aminotransferase In Complex With Th Domain Of Human Pex5p
authors K.Fodor, M.Wilmanns
compound source
Molecule: Serine--Pyruvate Aminotransferase
Chain: A, C
Synonym: Spt, Alanine--Glyoxylate Aminotransferase, Agt
Ec: 2.6.1.51, 2.6.1.44
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Agt1, Agxt, Spat
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Bl21 (De3) Ril
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Petm30

Molecule: Peroxisomal Targeting Signal 1 Receptor
Chain: B, D
Fragment: Tpr-Domain, Unp Residues 315-639
Synonym: Pts1 Receptor, Pts1r, Pts1-Bp, Peroxin-5, Peroxiso Terminal Targeting Signal Import Receptor, Peroxisome Recep
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Pex5, Pxr1
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Bl21 (De3) Ril
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Petm30
symmetry Space Group: P 1 21 1
R_factor 0.184 R_Free 0.239
crystal
cell
length a length b length c angle alpha angle beta angle gamma
59.367 99.156 127.698 90.00 96.66 90.00
method X-Ray Diffractionresolution 2.35 Å
ligand BTB, LLP enzyme Transferase E.C.2.6.1.51 BRENDA
note 3R9A supersedes 3IMZ
Gene
Ontology
ChainFunctionProcessComponent
A, C


Primary referenceMolecular requirements for peroxisomal targeting of alanine-glyoxylate aminotransferase as an essential determinant in primary hyperoxaluria type 1., Fodor K, Wolf J, Erdmann R, Schliebs W, Wilmanns M, PLoS Biol. 2012 Apr;10(4):e1001309. Epub 2012 Apr 17. PMID:22529745
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (453 Kb) [Save to disk]
  • Biological Unit Coordinates (3r9a.pdb1.gz) 447 Kb
  • LPC: Ligand-Protein Contacts for 3R9A
  • CSU: Contacts of Structural Units for 3R9A
  • Structure Factors (956 Kb)
  • Retrieve 3R9A in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3R9A from S2C, [Save to disk]
  • Re-refined 3r9a structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3R9A 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 3R9A
  • 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 3R9A, from MSDmotif at EBI
  • Fold representative 3r9a from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3r9a_B] [3r9a_D] [3r9a] [3r9a_C] [3r9a_A]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domain found in 3R9A: [TPR ] by SMART
  • Other resources with information on 3R9A
  • Community annotation for 3R9A 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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