Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asym./Biol. Unit
(-)Asym./Biol. Unit - sites
collapse expand < >
Image Asym./Biol. Unit
Asym./Biol. Unit  (Jmol Viewer)
Image Asym./Biol. Unit - sites
Asym./Biol. Unit - sites  (Jmol Viewer)

(-) Description

Title :  CRYSTAL STRUCTURE OF THE UNCHARACTERIZED MAF PROTEIN YCEF FROM E. COLI
 
Authors :  A. Dong, X. Xu, H. Cui, A. Tchigvintsev, R. Flick, G. Brown, A. Popovic, A. F. Yakunin, A. Savchenko
Date :  04 Mar 13  (Deposition) - 20 Mar 13  (Release) - 18 Dec 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.85
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Maf Protein, Putative Pyrophosphatase, Cell Cycle (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  A. Tchigvintsev, D. Tchigvintsev, R. Flick, A. Popovic, A. Dong, X. Xu G. Brown, W. Lu, H. Wu, H. Cui, L. Dombrowski, J. C. Joo, N. Beloglazova, J. Min, A. Savchenko, A. A. Caudy, J. D. Rabinowitz, A. G. Murzin, A. F. Yakunin
Biochemical And Structural Studies Of Conserved Maf Protein Revealed Nucleotide Pyrophosphatases With A Preference For Modified Nucleotides.
Chem. Biol. V. 20 1386 2013
PubMed-ID: 24210219  |  Reference-DOI: 10.1016/J.CHEMBIOL.2013.09.011

(-) Compounds

Molecule 1 - MAF-LIKE PROTEIN YCEF
    ChainsA, B
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidP15TVL
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    Expression System Vector TypePLASMID
    GeneYCEF, B1087, JW5155
    Organism ScientificESCHERICHIA COLI
    Organism Taxid83333
    StrainK12

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 15)

Asymmetric/Biological Unit (2, 15)
No.NameCountTypeFull Name
1GOL3Ligand/IonGLYCEROL
2UNX12Ligand/IonUNKNOWN ATOM OR ION

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWARESER A:8 , THR A:9 , SER A:10 , ARG A:13 , PRO A:29 , LYS A:52 , SER A:68 , HOH A:3109 , HOH A:3209BINDING SITE FOR RESIDUE GOL A 3001
2AC2SOFTWAREARG A:93 , HOH A:3122 , ARG B:167 , ALA B:179 , GLN B:182 , HOH B:318 , HOH B:342BINDING SITE FOR RESIDUE GOL B 201
3AC3SOFTWARESER B:8 , THR B:9 , ARG B:13 , LYS B:52BINDING SITE FOR RESIDUE GOL B 202

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4JHC)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Val B:139 -Arg B:140

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4JHC)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4JHC)

(-) Exons   (0, 0)

(no "Exon" information available for 4JHC)

(-) Sequences/Alignments

Asymmetric/Biological Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it)
Chain A from PDB  Type:PROTEIN  Length:192
                                                                                                                                                                                                                                
               SCOP domains d4jhca_ A: automated matches                                                                                                                                                                     SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeee..hhhhhhhhhhhh..eeee............hhhhhhhhhhhhhhhh........eeeeeeeeeee..eee....hhhhhhhhhhhhh..eeeeeeeeeeee.....eeeeeeeeeeee...hhhhhhhhhhhhh...........hhhhh.eeeee..hhhhhhh.hhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4jhc A   2 PKLILASTSPWRRALLEKLQISFECAAPEVDETPRSDESPRQLVLRLAQEKAQSLASRYPDHLIIGSDQVCVLDGEITGKPLTEENARLQLRKASGNIVTFYTGLALFNSANGHLQTEVEPFDVHFRHLSEAEIDNYVRKEHPLHCAGSFKSEGFGITLFERLEGRDPNTLVGLPLIALCQMLRREGKNPLM 193
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191  

Chain B from PDB  Type:PROTEIN  Length:182
                                                                                                                                                                                                                      
               SCOP domains d4jhcb_ B: automated matches                                                                                                                                                           SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeee...hhhhhhhhhh....eee.............hhhhhhhhhhhhhhhh.......eeeeeeeeeeee..eee.....hhhhhhhhhhh..eeeeeeeeeeee.....eeeeeeeeeeee...hhhhhhhhh.....hhhhh.eeeee..hhhhhhh.hhhhhhhhhhhh..hhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4jhc B   2 PKLILASTSPWRRALLEKLQISFECAAPEVDETPRSDESPRQLVLRLAQEKAQSLASRYPDHLIIGSDQVCVLDGEITGKPLEENARLQLRKASGNIVTFYTGLALFNSANGHLQTEVEPFDVHFRHLSEAEIDNYVRFKSEGFGITLFERLEGRDPNTLVGLPLIALCQMLRREGKNPLMG 194
                                    11        21        31        41        51        61        71        81 ||     92       102       112       122       132       152       162       172       182       192  
                                                                                                            83|                                                    140|                                           
                                                                                                             85                                                     151                                           

   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (1, 2)

Asymmetric/Biological Unit

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4JHC)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4JHC)

(-) Gene Ontology  (2, 2)

Asymmetric/Biological Unit(hide GO term definitions)

 Visualization

(-) Interactive Views

Asymmetric/Biological Unit
  Complete Structure
    Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
    WebMol | AstexViewer[tm]@PDBe
(Java Applets, require no local installation except for Java; loading may be slow)
    STRAP
(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    RasMol
(require local installation)
    Molscript (VRML)
(requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)
 
  Ligands, Modified Residues, Ions
    GOL  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    UNX  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Val B:139 - Arg B:140   [ RasMol ]  
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  4jhc
    Family and Domain InformationProDom | SYSTERS
    General Structural InformationGlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in MembranesOPM
    Protein SurfaceSURFACE
    Secondary StructureDSSP (structure derived) | HSSP (homology derived)
    Structural GenomicsGeneCensus
    Structural NeighboursCE | VAST
    Structure ClassificationCATH | Dali | SCOP
    Validation and Original DataBMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  YCEF_ECOLI | P0A729
    Comparative Protein Structure ModelsModBase
    Genomic InformationEnsembl
    Protein-protein InteractionDIP
    Sequence, Family and Domain InformationInterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  (no 'Enzyme Classificator' available)
    General Enzyme InformationBRENDA | EC-PDB | Enzyme | IntEnz
    PathwayKEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease InformationOMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related InformationGenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain InformationXDom
    Interatomic Contacts of Structural UnitsCSU
    Ligand-protein ContactsLPC
    Protein CavitiescastP
    Sequence and Secondary StructurePDBCartoon
    Structure AlignmentSTRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence BrowserSTING
 
Access by UniProt ID/Accession number
  YCEF_ECOLI | P0A729
    Protein Disorder PredictionDisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

(no "Entries Sharing at Least One Protein Chain" available for 4JHC)

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 4JHC)