Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asym./Biol. Unit - manually
(-)Asym./Biol. Unit
(-)Asym./Biol. Unit - sites
collapse expand < >
Image Asym./Biol. Unit - manually
Asym./Biol. Unit - manually  (Jmol Viewer)
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 PROX FROM ARCHEOGLOBUS FULGIDUS IN COMPLEX WITH GLYCINE BETAINE
 
Authors :  A. Schiefner, G. Holtmann, K. Diederichs, W. Welte, E. Bremer
Date :  30 Mar 04  (Deposition) - 14 Sep 04  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.10
Chains :  Asym./Biol. Unit :  A
Keywords :  Binding-Protein, Compatible Solutes, Cation-Pi Interactions, Non- Classical Hydrogen Bonds, Protein Binding (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. Schiefner, G. Holtmann, K. Diederichs, W. Welte, E. Bremer
Structural Basis For The Binding Of Compatible Solutes By Prox From The Hyperthermophilic Archaeon Archaeoglobus Fulgidus.
J. Biol. Chem. V. 279 48270 2004
PubMed-ID: 15308642  |  Reference-DOI: 10.1074/JBC.M403540200

(-) Compounds

Molecule 1 - OSMOPROTECTION PROTEIN (PROX)
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PASK-IBA6
    Expression System Strain: BL21(CODON PLUS RIL)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: PROX
    Mutation: YES
    Organism Scientific: ARCHAEOGLOBUS FULGIDUS
    Organism Taxid: 224325
    Strain: DSM 4304

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 1)

Asymmetric/Biological Unit (1, 1)
No.NameCountTypeFull Name
1BET1Ligand/IonTRIMETHYL GLYCINE

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELYS A:13 , PHE A:15 , TYR A:63 , THR A:66 , ASP A:109 , TYR A:111 , ARG A:149 , TYR A:190 , TYR A:214BINDING SITE FOR RESIDUE BET A 301

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1SW2)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1SW2)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1SW2)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1SW2)

(-) Exons   (0, 0)

(no "Exon" information available for 1SW2)

(-) 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:270
 aligned with O29280_ARCFU | O29280 from UniProtKB/TrEMBL  Length:292

    Alignment length:270
                                    32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292
         O29280_ARCFU    23 ERVVIGSKPFNEQYILANMIAILLEENGYKAEVKEGLGGTLVNYEALKRNDIQLYVEYTGTAYNVILRKQPPELWDQQYIFDEVKKGLLEADGVVVAAKLGFRDDYALAVRADWAEENGVEKISDLAEFADQLVFGSDPEFASRPDGLPQIKKVYGFEFKEVKQMEPTLMYEAIKNKQVDVIPAYTTDSRVDLFNLKILEDDKGALPPYDAIIIVNGNTAKDEKLISVLKLLEDRIDTDTMRALNYQYDVEKKDAREIAMSFLKEQGLVK 292
               SCOP domains d1sw2a_ A: Osmoprotection protein ProX                                                                                                                                                                                                                                         SCOP domains
               CATH domains 1sw2A01 A:6-109,A:214-275 Periplasmic binding protein-like II                                           1sw2A02 A:110-213 Osmoprotection protein (prox); domain 2                                               1sw2A01 A:6-109,A:214-275 Periplasmic binding protein-like II  CATH domains
               Pfam domains OpuAC-1sw2A01 A:6-270                                                                                                                                                                                                                                                    ----- Pfam domains
         Sec.struct. author .eeee....hhhhhhhhhhhhhhhhhh..eeee.....hhhhhhhhhhh....eeeeehhhhhhh..........hhhhhhhhhhhhhhhhhh.eeeeeeeee..eeeeeehhhhhhhh...hhhhhhhhhh.eeee.........hhhhhhhhhh....eeee...hhhhhhhhh....eeeee...hhhhhh.eee...........eeeeee..hhhhhhhhhhhhhh.....hhhhhhhhhhhhhh...hhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1sw2 A   6 ERVVIGSKPFNEQYILANMIAILLEENGYKAEVKEGLGGTLVNYEALKRNDIQLYVEYTGTAYNVILRKQPPELWDQQYIFDEVKKGLLEADGVVVAAKLGFRDDYALAVRADWAEENGVEKISDLAEFADQLVFGSDPEFASRPDGLPQIKKVYGFEFKEVKQMEPTLMYEAIKNKQVDVIPAYTTDSRVDLFNLKILEDDKGALPPYDAIIIVNGNTAKDEKLISVLKLLEDRIDTDTMRALNYQYDVEKKDAREIAMSFLKEQGLVK 275
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275
   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) (23833)

(-) CATH Domains  (2, 2)

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

(-) Pfam Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Clan: PBP (391)

(-) Gene Ontology  (3, 3)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (O29280_ARCFU | O29280)
molecular function
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0005215    transporter activity    Enables the directed movement of substances (such as macromolecules, small molecules, ions) into, out of or within a cell, or between cells.
biological process
    GO:0006810    transport    The directed movement of substances (such as macromolecules, small molecules, ions) or cellular components (such as complexes and organelles) into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter, pore or motor protein.

 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
    BET  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 1sw2)
 

(-) 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 | Asym./Biol. Unit - sites 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
  1sw2
    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
  O29280_ARCFU | O29280
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/TrEMBL
 
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
  O29280_ARCFU | O29280
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/TrEMBL
        O29280_ARCFU | O29280: 1sw1 1sw4 1sw5 3mam

(-) Related Entries Specified in the PDB File

1sw1 CRYSTAL STRUCTURE OF PROX FROM ARCHEOGLOBUS FULGIDUS IN COMPLEX WITH PROLINE BETAINE