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(-) Description

Title :  CRYSTAL STRUCTURE OF YEAST HYPOTHETICAL PROTEIN YBL036C-SELENOMET CRYSTAL
 
Authors :  S. Eswaramoorthy, S. Swaminathan, S. K. Burley, New York Sgx Resear For Structural Genomics (Nysgxrc)
Date :  18 Aug 99  (Deposition) - 02 Sep 99  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym./Biol. Unit :  A
Keywords :  Tim Barrel, Yeast, Pyridoxal-5'-Phosphate, Selenomethionine, Mad, Structural Genomics, Psi, Protein Structure Initiative, New York Sgx Research Center For Structural Genomics, Nysgxrc (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. Eswaramoorthy, S. Gerchman, V. Graziano, H. Kycia, F. W. Studier, S. Swaminathan
Structure Of A Yeast Hypothetical Protein Selected By A Structural Genomics Approach.
Acta Crystallogr. , Sect. D V. 59 127 2003
PubMed-ID: 12499548  |  Reference-DOI: 10.1107/S0907444902018012

(-) Compounds

Molecule 1 - PROTEIN (YEAST HYPOTHETICAL PROTEIN, SELENOMET)
    Chains: A
    Engineered: YES
    Expression System: SACCHAROMYCES CEREVISIAE
    Expression System Common: BAKER'S YEAST
    Expression System Plasmid: PET-13A B834(DE3)
    Expression System Taxid: 4932
    Expression System Vector Type: PLASMID
    Organism Common: BAKER'S YEAST
    Organism Scientific: SACCHAROMYCES CEREVISIAE
    Organism Taxid: 4932
    Strain: YBL 036C

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 4)

Asymmetric/Biological Unit (2, 4)
No.NameCountTypeFull Name
1MSE3Mod. Amino AcidSELENOMETHIONINE
2PLP1Ligand/IonPYRIDOXAL-5'-PHOSPHATE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELYS A:49 , ASN A:70 , ILE A:91 , MSE A:223 , SER A:224 , ARG A:239 , GLY A:241 , THR A:242 , HOH A:292 , HOH A:332 , HOH A:351 , HOH A:355 , HOH A:425BINDING SITE FOR RESIDUE PLP A 258
2SITAUTHORLYS A:49 , ASN A:70 , SER A:224 , ARG A:239 , THR A:242RESIDUES INTERACTING WITH THE CO-FACTOR PLP

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1CT5)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1CT5)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1CT5)

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1UPF0001PS01211 Uncharacterized protein family UPF0001 signature.PLPHP_YEAST88-102  1A:88-102

(-) Exons   (1, 1)

Asymmetric/Biological Unit (1, 1)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1YBL036C1YBL036C.1II:151223-150450774PLPHP_YEAST1-2572571A:3-246 (gaps)244

(-) 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:228
 aligned with PLPHP_YEAST | P38197 from UniProtKB/Swiss-Prot  Length:257

    Alignment length:244
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242    
          PLPHP_YEAST     3 TGITYDEDRKTQLIAQYESVREVVNAEAKNVHVNENASKILLLVVSKLKPASDIQILYDHGVREFGENYVQELIEKAKLLPDDIKWHFIGGLQTNKCKDLAKVPNLYSVETIDSLKKAKKLNESRAKFQPDCNPILCNVQINTSHEDQKSGLNNEAEIFEVIDFFLSEECKYIKLNGLMTIGSWNVSHEDSKENRDFATLVEWKKKIDAKFGTSLKLSMGMSADFREAIRQGTAEVRIGTDIFG 246
               SCOP domains d1ct5a_ A: Hypothetical protein        ybl036c                                                                                                                                                                                                       SCOP domains
               CATH domains 1ct5A00 A:3-246 Alanine racemas       e                                                                                                                                                                                                              CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......hhhhhhhhhhhhhhhhhhhhhhhh.-------..eeee......hhhhhhhhhh...eeee..hhhhhhhhhh.....eeee........hhhhhh...eeee.....hhhhhhhhhhhhhhh.....eeeeee..............hhhhhhhhhhh.......eeeeeee.....---------.hhhhhhhhhhhhhhhhh....eee......hhhhhh....eeee...... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------UPF0001        ------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
               Transcript 1 Exon 1.1  PDB: A:3-246 (gaps) UniProt: 1-257 [INCOMPLETE]                                                                                                                                                                                            Transcript 1
                 1ct5 A   3 TGITYDEDRKTQLIAQYESVREVVNAEAKNV-------KILLLVVSKLKPASDIQILYDHGVREFGENYVQELIEKAKLLPDDIKWHFIGGLQTNKCKDLAKVPNLYSVETIDSLKKAKKLNESRAKFQPDCNPILCNVQINTSHEDQKSGLNNEAEIFEVIDFFLSEECKYIKLNGLmTIGSW---------NRDFATLVEWKKKIDAKFGTSLKLSmGmSADFREAIRQGTAEVRIGTDIFG 246
                                    12        22        32|       42        52        62        72        82        92       102       112       122       132       142       152       162       172       182   |     -   |   202       212       222|      232       242    
                                                         33      41                                                                                                                                         181-MSE6       196                      221-MSE                     
                                                                                                                                                                                                                                                      223-MSE
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  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
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (1, 1)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1CT5)

(-) Gene Ontology  (4, 4)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (PLPHP_YEAST | P38197)
molecular function
    GO:0030170    pyridoxal phosphate binding    Interacting selectively and non-covalently with pyridoxal 5' phosphate, 3-hydroxy-5-(hydroxymethyl)-2-methyl4-pyridine carboxaldehyde 5' phosphate, the biologically active form of vitamin B6.
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.
cellular component
    GO:0005575    cellular_component    The part of a cell, extracellular environment or virus in which a gene product is located. A gene product may be located in one or more parts of a cell and its location may be as specific as a particular macromolecular complex, that is, a stable, persistent association of macromolecules that function together.
    GO:0005622    intracellular    The living contents of a cell; the matter contained within (but not including) the plasma membrane, usually taken to exclude large vacuoles and masses of secretory or ingested material. In eukaryotes it includes the nucleus and cytoplasm.

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 Related Entries

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

UniProtKB/Swiss-Prot
        PLPHP_YEAST | P38197: 1b54

(-) Related Entries Specified in the PDB File

1b54 1B54 IS THE WILD TYPE OF THE SAME PROTEIN RELATED ID: NYSGXRC-P007 RELATED DB: TARGETDB