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(-) Description

Title :  CRYSTAL STRUCTURE OF AN HYPOTHETICAL PROTEIN
 
Authors :  Structural Genomix
Date :  01 Dec 03  (Deposition) - 30 Dec 03  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.76
Chains :  Asym./Biol. Unit :  A
Keywords :  Structural Genomics, Unknown Function (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. Badger, J. M. Sauder, J. M. Adams, S. Antonysamy, K. Bain, M. G. Bergseid, S. G. Buchanan, M. D. Buchanan, Y. Batiyenko, J. A. Christopher, S. Emtage, A. Eroshkina, I. Feil, E. B. Furlong, K. S. Gajiwala, X. Gao, D. He, J. Hendle, A. Huber, K. Hoda, P. Kearins, C. Kissinger, B. Laubert, H. A. Lewis, J. Lin, K. Loomis, D. Lorimer, G. Louie, M. Maletic, C. D. Marsh, I. Miller, J. Molinari, H. J. Muller-Dieckmann, J. M. Newman, B. W. Noland, B. Pagarigan, F. Park, T. S. Peat, K. W. Post, S. Radojicic, A. Ramos, R. Romero, M. E. Rutter, W. E. Sanderson, K. D. Schwinn, J. Tresser, J. Winhoven, T. A. Wright, L. Wu, J. Xu, T. J. Harris
Structural Analysis Of A Set Of Proteins Resulting From A Bacterial Genomics Project
Proteins V. 60 787 2005
PubMed-ID: 16021622  |  Reference-DOI: 10.1002/PROT.20541
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PROTEIN YBHB
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: YBHB, B0773
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 562

 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
1ACT1Ligand/IonACETATE ION
2MSE4Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:52 , TRP A:61 , HIS A:63 , ALA A:107 , PRO A:108 , TYR A:116 , HOH A:260BINDING SITE FOR RESIDUE ACT A 169

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1VI3)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1VI3)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1VI3)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1VI3)

(-) Exons   (0, 0)

(no "Exon" information available for 1VI3)

(-) 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:160
 aligned with YBHB_ECOLI | P12994 from UniProtKB/Swiss-Prot  Length:158

    Alignment length:160
                             1                                                                                                                                                          158  
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149        |-
           YBHB_ECOLI     - -MKLISNDLRDGDKLPHRHVFNGMGYDGDNISPHLAWDDVPAGTKSFVVTCYDPDAPTGSGWWHWVVVNLPADTRVLPQGFGSGLVAMPDGVLQTRTDFGKTGYDGAAPPKGETHRYIFTVHALDIERIDVDEGASGAMVGFNVHFHSLASASITAMFS-   -
               SCOP domains d1vi3a_ A: Hypothetical protein YbhB                                                                                                                             SCOP domains
               CATH domains 1vi3A00 A:0-159 Phosphatidylethanolamine-binding Protein;                                                                                                        CATH domains
               Pfam domains -----------PBP-1vi3A01 A:11-158                                                                                                                                - Pfam domains
         Sec.struct. author ..eee..........hhhhh..............eeee.......eeeeeeee........eeeeeeeeee....ee...............ee...................eeeeeeeeeee...........hhhhhhhhhhhheeeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1vi3 A   0 SLKLISNDLRDGDKLPHRHVFNGmGYDGDNISPHLAWDDVPAGTKSFVVTCYDPDAPTGSGWWHWVVVNLPADTRVLPQGFGSGLVAmPDGVLQTRTDFGKTGYDGAAPPKGETHRYIFTVHALDIERIDVDEGASGAmVGFNVHFHSLASASITAmFSE 159
                                     9        19   |    29        39        49        59        69        79       |89        99       109       119       129       139       149      |159
                                                  23-MSE                                                          87-MSE                                            138-MSE           156-MSE
   Legend:   → Mismatch (orange background)
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  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
(-)
Class: All beta proteins (24004)

(-) CATH Domains  (1, 1)

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

(-) Pfam Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Clan: no clan defined [family: PBP] (9)

(-) Gene Ontology  (1, 1)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (YBHB_ECOLI | P12994)
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

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  1vi3
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  YBHB_ECOLI | P12994
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 Related Entries

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

UniProtKB/Swiss-Prot
        YBHB_ECOLI | P12994: 1fjj

(-) Related Entries Specified in the PDB File

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