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

(-) Description

Title :  CRYSTAL STRUCTURE OF E. COLI YHBY
 
Authors :  G. J. Ostheimer, A. Barkan, B. W. Matthews
Date :  02 May 02  (Deposition) - 15 May 02  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.50
Chains :  Asym./Biol. Unit :  A
Keywords :  Putative Rna-Binding Protein; Putative Translation Factor, Rna Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  G. J. Ostheimer, A. Barkan, B. W. Matthews
Crystal Structure Of E. Coli Yhby: A Representative Of A Novel Class Of Rna Binding Proteins
Structure V. 10 1593 2002
PubMed-ID: 12429100  |  Reference-DOI: 10.1016/S0969-2126(02)00886-9
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - HYPOTHETICAL PROTEIN YHBY
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET28B
    Expression System Strain: BL21 (DE3) GOLD
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: YHBY
    Mutation: YES
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 562
    Synonym: YHBY

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 1LN4)

(-) Sites  (0, 0)

(no "Site" information available for 1LN4)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1LN4)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1LN4)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1LN4)

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1CRMPS51295 CRM domain profile.YHBY_ECO571-97  1A:1-96
YHBY_ECOL61-97  1A:1-96
YHBY_ECOLI1-97  1A:1-96
YHBY_SHIFL1-97  1A:1-96

(-) Exons   (0, 0)

(no "Exon" information available for 1LN4)

(-) 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:98
 aligned with YHBY_ECO57 | P0AGK6 from UniProtKB/Swiss-Prot  Length:97

    Alignment length:98
                                                                                                                           97 
                                    10        20        30        40        50        60        70        80        90      | 
            YHBY_ECO57    1 MNLSTKQKQHLKGLAHPLKPVVLLGSNGLTEGVLAEIEQALEHHELIKVKIATEDRETKTLIVEAIVRETGACNVQVIGKTLVLYRPTKERKISLPR-  -
               SCOP domains d1ln4a_ A: hypothetical protein YhbY                                                               SCOP domains
               CATH domains 1ln4A00 A:1-98 YhbY-like                                                                           CATH domains
               Pfam domains --CRS1_YhbY-1ln4A01 A:3-86                                                            ------------ Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhh.....eee.....hhhhhhhhhhhhhhhheeeeee...hhhhhhhhhhhhhhhhh.eeeeee..eeeee............. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (2) -------------------------------------------------------------------------------------------------- PROSITE (2)
                PROSITE (3) -------------------------------------------------------------------------------------------------- PROSITE (3)
                PROSITE (4) CRM  PDB: A:1-96 UniProt: 1-97                                                                   - PROSITE (4)
                 Transcript -------------------------------------------------------------------------------------------------- Transcript
                  1ln4 A  1 MDLSTKQKQHLKGLAHPLKPVVLLGSNGLTEGVLAEIEQALEHHELIKVKIATEDRETKTLIVEAIVRETGACNVQVIGKTLVLYRPTKERKISLPLE 98
                                    10        20        30        40        50        60        70        80        90        


Chain A from PDB  Type:PROTEIN  Length:98
 aligned with YHBY_ECOL6 | P0AGK5 from UniProtKB/Swiss-Prot  Length:97

    Alignment length:98
                                                                                                                           97 
                                    10        20        30        40        50        60        70        80        90      | 
            YHBY_ECOL6    1 MNLSTKQKQHLKGLAHPLKPVVLLGSNGLTEGVLAEIEQALEHHELIKVKIATEDRETKTLIVEAIVRETGACNVQVIGKTLVLYRPTKERKISLPR-  -
               SCOP domains d1ln4a_ A: hypothetical protein YhbY                                                               SCOP domains
               CATH domains 1ln4A00 A:1-98 YhbY-like                                                                           CATH domains
               Pfam domains --CRS1_YhbY-1ln4A01 A:3-86                                                            ------------ Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhh.....eee.....hhhhhhhhhhhhhhhheeeeee...hhhhhhhhhhhhhhhhh.eeeeee..eeeee............. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE CRM  PDB: A:1-96 UniProt: 1-97                                                                   - PROSITE
                 Transcript -------------------------------------------------------------------------------------------------- Transcript
                  1ln4 A  1 MDLSTKQKQHLKGLAHPLKPVVLLGSNGLTEGVLAEIEQALEHHELIKVKIATEDRETKTLIVEAIVRETGACNVQVIGKTLVLYRPTKERKISLPLE 98
                                    10        20        30        40        50        60        70        80        90        


Chain A from PDB  Type:PROTEIN  Length:98
 aligned with YHBY_ECOLI | P0AGK4 from UniProtKB/Swiss-Prot  Length:97

    Alignment length:98
                                                                                                                           97 
                                    10        20        30        40        50        60        70        80        90      | 
            YHBY_ECOLI    1 MNLSTKQKQHLKGLAHPLKPVVLLGSNGLTEGVLAEIEQALEHHELIKVKIATEDRETKTLIVEAIVRETGACNVQVIGKTLVLYRPTKERKISLPR-  -
               SCOP domains d1ln4a_ A: hypothetical protein YhbY                                                               SCOP domains
               CATH domains 1ln4A00 A:1-98 YhbY-like                                                                           CATH domains
               Pfam domains --CRS1_YhbY-1ln4A01 A:3-86                                                            ------------ Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhh.....eee.....hhhhhhhhhhhhhhhheeeeee...hhhhhhhhhhhhhhhhh.eeeeee..eeeee............. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (2) CRM  PDB: A:1-96 UniProt: 1-97                                                                   - PROSITE (2)
                 Transcript -------------------------------------------------------------------------------------------------- Transcript
                  1ln4 A  1 MDLSTKQKQHLKGLAHPLKPVVLLGSNGLTEGVLAEIEQALEHHELIKVKIATEDRETKTLIVEAIVRETGACNVQVIGKTLVLYRPTKERKISLPLE 98
                                    10        20        30        40        50        60        70        80        90        


Chain A from PDB  Type:PROTEIN  Length:98
 aligned with YHBY_SHIFL | P0AGK7 from UniProtKB/Swiss-Prot  Length:97

    Alignment length:98
                                                                                                                           97 
                                    10        20        30        40        50        60        70        80        90      | 
            YHBY_SHIFL    1 MNLSTKQKQHLKGLAHPLKPVVLLGSNGLTEGVLAEIEQALEHHELIKVKIATEDRETKTLIVEAIVRETGACNVQVIGKTLVLYRPTKERKISLPR-  -
               SCOP domains d1ln4a_ A: hypothetical protein YhbY                                                               SCOP domains
               CATH domains 1ln4A00 A:1-98 YhbY-like                                                                           CATH domains
               Pfam domains --CRS1_YhbY-1ln4A01 A:3-86                                                            ------------ Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhh.....eee.....hhhhhhhhhhhhhhhheeeeee...hhhhhhhhhhhhhhhhh.eeeeee..eeeee............. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (2) -------------------------------------------------------------------------------------------------- PROSITE (2)
                PROSITE (3) CRM  PDB: A:1-96 UniProt: 1-97                                                                   - PROSITE (3)
                 Transcript -------------------------------------------------------------------------------------------------- Transcript
                  1ln4 A  1 MDLSTKQKQHLKGLAHPLKPVVLLGSNGLTEGVLAEIEQALEHHELIKVKIATEDRETKTLIVEAIVRETGACNVQVIGKTLVLYRPTKERKISLPLE 98
                                    10        20        30        40        50        60        70        80        90
   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
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (1, 1)

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

(-) Pfam Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Clan: no clan defined [family: CRS1_YhbY] (1)

(-) Gene Ontology  (3, 6)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (YHBY_ECO57 | P0AGK6)
molecular function
    GO:0003723    RNA binding    Interacting selectively and non-covalently with an RNA molecule or a portion thereof.

Chain A   (YHBY_ECOLI | P0AGK4)
molecular function
    GO:0003723    RNA binding    Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
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.

Chain A   (YHBY_SHIFL | P0AGK7)
molecular function
    GO:0003723    RNA binding    Interacting selectively and non-covalently with an RNA molecule or a portion thereof.

Chain A   (YHBY_ECOL6 | P0AGK5)
molecular function
    GO:0003723    RNA binding    Interacting selectively and non-covalently with an RNA molecule or a portion thereof.

 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
(no "Ligands, Modified Residues, Ions" information available for 1ln4)
 
  Sites
(no "Sites" information available for 1ln4)
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 1ln4)
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym./Biol. Unit PNG format ](automatic orientation, automatically generated)
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick
[ mono PDF format | stereo PDF format ](default orientation, automatically generated)

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  1ln4
    Family and Domain Information: ProDom | SYSTERS
    General Structural Information: GlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in Membranes: OPM
    Protein Surface: SURFACE
    Secondary Structure: DSSP (structure derived) | HSSP (homology derived)
    Structural Genomics: GeneCensus
    Structural Neighbours: CE | VAST
    Structure Classification: CATH | Dali | SCOP
    Validation and Original Data: BMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  YHBY_ECO57 | P0AGK6
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
  YHBY_ECOL6 | P0AGK5
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
  YHBY_ECOLI | P0AGK4
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
  YHBY_SHIFL | P0AGK7
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  (no 'Enzyme Classificator' available)
    General Enzyme Information: BRENDA | EC-PDB | Enzyme | IntEnz
    Pathway: KEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease Information: OMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related Information: GenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain Information: XDom
    Interatomic Contacts of Structural Units: CSU
    Ligand-protein Contacts: LPC
    Protein Cavities: castP
    Sequence and Secondary Structure: PDBCartoon
    Structure Alignment: STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence Browser: STING
 
Access by UniProt ID/Accession number
  YHBY_ECO57 | P0AGK6
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)
  YHBY_ECOL6 | P0AGK5
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)
  YHBY_ECOLI | P0AGK4
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)
  YHBY_SHIFL | P0AGK7
    Protein Disorder Prediction: DisEMBL | 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 1LN4)

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 1LN4)