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 :  STRUCTURE OF YGR205W PROTEIN.
 
Authors :  I. Li De La Sierra-Gallay, H. Van Tilbeurgh
Date :  19 Feb 03  (Deposition) - 12 Dec 03  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.25
Chains :  Asym./Biol. Unit :  A
Keywords :  Yeast Protein, Atp Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  I. Li De La Sierra-Gallay, B. Collinet, M. Graille, S. Quevillon-Cheruel, D. Liger, P. Minard, K. Blondeau, G. Henckes, R. Aufrere, N. Leulliot, C. Z. Zhou, I. Sorrel, J. L. Ferrer, A. Poupon, J. Janin, H. Van Tilbeurgh
Crystal Structure Of The Ygr205W Protein From Saccharomyces Cerevisiae: Close Structural Resemblance To E. Coli Pantothenate Kinase
Proteins: Struct. , Funct. , V. 54 776 2004 Genet.
PubMed-ID: 14997573  |  Reference-DOI: 10.1002/PROT.10596

(-) Compounds

Molecule 1 - HYPOTHETICAL 33.3 KDA PROTEIN IN ADE3-SER2 INTERGENIC REGION
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    Organism CommonBAKER'S YEAST
    Organism ScientificSACCHAROMYCES CEREVISIAE
    Organism Taxid4932
    Other DetailsCLONED GENE
    StrainS288C
    SynonymYGR205W

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 5)

Asymmetric/Biological Unit (2, 5)
No.NameCountTypeFull Name
1GOL3Ligand/IonGLYCEROL
2SO42Ligand/IonSULFATE ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLN A:40 , GLY A:41 , SER A:42 , GLY A:43 , LYS A:44 , SER A:45 , GLN A:170 , GLY A:171 , ILE A:172 , HOH A:2073 , HOH A:2074BINDING SITE FOR RESIDUE SO4 A 501
2AC2SOFTWARETYR A:74 , ARG A:96 , LYS A:133 , ASN A:174BINDING SITE FOR RESIDUE SO4 A 502
3AC3SOFTWARETHR A:284 , LYS A:285 , THR A:286BINDING SITE FOR RESIDUE GOL A 504
4AC4SOFTWAREGLN A:108 , LEU A:111 , ASN A:112 , LEU A:195 , ASN A:199 , GLU A:201BINDING SITE FOR RESIDUE GOL A 505

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1ODF)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Leu A:151 -Pro A:152

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1ODF)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1ODF)

(-) Exons   (1, 1)

Asymmetric/Biological Unit (1, 1)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1YGR205W1YGR205W.1VII:909218-910090873TDA10_YEAST1-2902901A:5-290 (gaps)286

(-) 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:280
 aligned with TDA10_YEAST | P42938 from UniProtKB/Swiss-Prot  Length:290

    Alignment length:286
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284      
          TDA10_YEAST     5 SKTVLDYTIEFLDKYIPEWFETGNKCPLFIFFSGPQGSGKSFTSIQIYNHLMEKYGGEKSIGYASIDDFYLTHEDQLKLNEQFKNNKLLQGRGLPGTHDMKLLQEVLNTIFNNNEHPDQDTVVLPKYDKSQFKGEGDRCPTGQKIKLPVDIFILEGWFLGFNPILQGIENNDLLTGDMVDVNAKLFFYSDLLWRNPEIKSLGIVFTTDNINNVYGWRLQQEHELISKVGKGMTDEQVHAFVDRYMPSYKLYLNDFVRSESLGSIATLTLGIDSNRNVYSTKTRCIE 290
               SCOP domains d1odfa_ A: Hypothetical protein Ygr205W                                                                                                                                                                                                                                                        SCOP domains
               CATH domains 1odfA00 A:5-290 P-loop containing nucleotide triphosphate hydrolases                                                                                                                                                                                                                           CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhh......eeeeee.....hhhhhhhhhhhhhhhhhhhhh.eeeee.hhh..hhhhhhhhhhhh..hhhhh........hhhhhhhhhhhhh.------..eeee..ee..hhhhh.ee....eeee....eeeeee....................hhhhhhhhhhhhhhhh.......eeeeeeee...hhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhh.....eeeeeee.....eeeeeee... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
               Transcript 1 Exon 1.1  PDB: A:5-290 (gaps) UniProt: 1-290 [INCOMPLETE]                                                                                                                                                                                                                                      Transcript 1
                 1odf A   5 SKTVLDYTIEFLDKYIPEWFETGNKCPLFIFFSGPQGSGKSFTSIQIYNHLMEKYGGEKSIGYASIDDFYLTHEDQLKLNEQFKNNKLLQGRGLPGTHDMKLLQEVLNTIFN------QDTVVLPKYDKSQFKGEGDRCPTGQKIKLPVDIFILEGWFLGFNPILQGIENNDLLTGDMVDVNAKLFFYSDLLWRNPEIKSLGIVFTTDNINNVYGWRLQQEHELISKVGKGMTDEQVHAFVDRYMPSYKLYLNDFVRSESLGSIATLTLGIDSNRNVYSTKTRCIE 290
                                    14        24        34        44        54        64        74        84        94       104       114 |     124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284      
                                                                                                                                         116    123                                                                                                                                                                       

   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, 1)

Asymmetric/Biological Unit

(-) CATH Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1ODF)

(-) Gene Ontology  (12, 12)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (TDA10_YEAST | P42938)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0016301    kinase activity    Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule.
    GO:0000166    nucleotide binding    Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
    GO:0016740    transferase activity    Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
    GO:0004849    uridine kinase activity    Catalysis of the reaction: ATP + uridine = ADP + UMP.
biological process
    GO:0008150    biological_process    Any process specifically pertinent to the functioning of integrated living units: cells, tissues, organs, and organisms. A process is a collection of molecular events with a defined beginning and end.
    GO:0016310    phosphorylation    The process of introducing a phosphate group into a molecule, usually with the formation of a phosphoric ester, a phosphoric anhydride or a phosphoric amide.
    GO:0006206    pyrimidine nucleobase metabolic process    The chemical reactions and pathways involving pyrimidine nucleobases, 1,3-diazine, organic nitrogenous bases.
    GO:0043097    pyrimidine nucleoside salvage    Any process that generates a pyrimidine nucleoside, one of a family of organic molecules consisting of a pyrimidine base covalently bonded to a sugar ribose, from derivatives of it, without de novo synthesis.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
    GO:0005634    nucleus    A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.

 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 ]
    SO4  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
    AC4  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Leu A:151 - Pro A:152   [ 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
  1odf
    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
  TDA10_YEAST | P42938
    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
  TDA10_YEAST | P42938
    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 1ODF)

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 1ODF)