4DA1 Hydrolase date Jan 12, 2012
title Crystal Structure Of Branched-Chain Alpha-Ketoacid Dehydroge Phosphatase With Mg (II) Ions At The Active Site
authors C.A.Brautigam, J.L.Chuang, D.T.Chuang
compound source
Molecule: Protein Phosphatase 1k, Mitochondrial
Chain: A
Fragment: Truncated Phosphatase Protein (Unp Residues 84-36
Synonym: Pp2c Domain-Containing Protein Phosphatase 1k, Pp2 Mitochondrial Protein, Pp2c-Type Mitochondrial Phosphoprote Phosphatase, Ptmp, Protein Phosphatase 2c Isoform Kappa, Pp
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Ppm1k, Pp2cm
Expression_system: Escherichia Coli
Expression_system_taxid: 562
symmetry Space Group: P 31 2 1
R_factor 0.177 R_Free 0.205
length a length b length c angle alpha angle beta angle gamma
125.276 125.276 61.660 90.00 90.00 120.00
method X-Ray Diffractionresolution 2.38 Å
ligand BME, MG enzyme Hydrolase E.C. BRENDA

Primary referenceStructural and biochemical characterization of human mitochondrial branched-chain alpha-ketoacid dehydrogenase phosphatase., Wynn RM, Li J, Brautigam CA, Chuang JL, Chuang DT, J Biol Chem. 2012 Mar 16;287(12):9178-92. Epub 2012 Jan 30. PMID:22291014
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (93 Kb) [Save to disk]
  • Biological Unit Coordinates (4da1.pdb1.gz) 87 Kb
  • LPC: Ligand-Protein Contacts for 4DA1
  • CSU: Contacts of Structural Units for 4DA1
  • Structure Factors (280 Kb)
  • Retrieve 4DA1 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 4DA1 from S2C, [Save to disk]
  • Re-refined 4da1 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 4DA1 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 4DA1
  • 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 4DA1, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1k4da1, region A:1-118 [Jmol] [rasmolscript] [script source]
        - Domain d1t4da1, region A:1-133,A:355-367 [Jmol] [rasmolscript] [script source]
        - Domain d1d4da1, region A:4-102 [Jmol] [rasmolscript] [script source]
  • Fold representative 4da1 from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [4da1] [4da1_A]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domains found in 4DA1: [PP2C_SIG] [PP2Cc] [UBQ ] by SMART
  • Other resources with information on 4DA1
  • Community annotation for 4DA1 at PDBWiki (http://pdbwiki.org)
  • Movements, Movies and Images
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