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 :  STRUCTURE ANALYSIS OF PROX IN COMPLEX WITH PROLINE BETAINE
 
Authors :  A. Schiefner, J. Breed, L. Bosser, S. Kneip, J. Gade, G. Holtmann, K. Diederichs, W. Welte, E. Bremer
Date :  30 Oct 03  (Deposition) - 24 Feb 04  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.05
Chains :  Asym./Biol. Unit :  A
Keywords :  Periplasmic Binding Protein, Cation-Pi Interactions, Tryptophan Box, Protein Binding (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. Schiefner, J. Breed, L. Bosser, S. Kneip, J. Gade, G. Holtmann, K. Diederichs, W. Welte, E. Bremer
Cation-Pi Interactions As Determinants For Binding Of The Compatible Solutes Glycine Betaine And Proline Betaine By The Periplasmic Ligand-Binding Protein Prox From Escherichia Coli
J. Biol. Chem. V. 279 5588 2004
PubMed-ID: 14612446  |  Reference-DOI: 10.1074/JBC.M309771200
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - GLYCINE BETAINE-BINDING PERIPLASMIC PROTEIN
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PSK7
    Expression System Strain: PD141
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: PROX
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 562
    Synonym: PERIPLASMIC LIGAND-BINDING PROTEIN PROX

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (2, 2)
No.NameCountTypeFull Name
1PBE1Ligand/Ion1,1-DIMETHYL-PROLINIUM
2UNX1Ligand/IonUNKNOWN ATOM OR ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:124 , ASN A:126 , ASP A:128 , LYS A:130 , ASP A:132 , HOH A:1338BINDING SITE FOR RESIDUE UNX A 1310
2AC2SOFTWARETYR A:46 , TRP A:65 , LEU A:68 , HIS A:69 , TRP A:140 , GLY A:141 , CYS A:142 , TRP A:188BINDING SITE FOR RESIDUE PBE A 1001

(-) SS Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1A:136 -A:142

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Thr A:66 -Pro A:67
2Thr A:189 -Pro A:190

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1R9Q)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1R9Q)

(-) Exons   (0, 0)

(no "Exon" information available for 1R9Q)

(-) 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:309
 aligned with PROX_ECO57 | P0AFM3 from UniProtKB/Swiss-Prot  Length:330

    Alignment length:309
                                    31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321         
           PROX_ECO57    22 ADLPGKGITVNPVQSTITEETFQTLLVSRALEKLGYTVNKPSEVDYNVGYTSLASGDATFTAVNWTPLHDNMYEAAGGDKKFYREGVFVNGAAQGYLIDKKTADQYKITNIAQLKDPKIAKLFDTNGDGKADLTGCNPGWGCEGAINHQLAAYELTNTVTHNQGNYAAMMADTISRYKEGKPVFYYTWTPYWVSNELKPGKDVVWLQVPFSALPGDKNADTKLPNGANYGFPVSTMHIVANKAWAEKNPAAAKLFAIMQLPVADINAQNAIMHDGKASEGDIQGHVDGWIKAHQQQFDGWVNEALAAQK 330
               SCOP domains d1r9qa_ A: Glycine betaine-binding periplasmic protein ProX                                                                                                                                                                                                                                                           SCOP domains
               CATH domains 1r9qA01 A:1-91,A:233-309 Periplasmic binding protein-like II                               1r9qA02 A:92-232 Glycine betaine-binding periplasmic protein; domain 2                                                                       1r9qA01 A:1-91,A:233-309 Periplasmic binding protein-like II                  CATH domains
               Pfam domains -------OpuAC-1r9qA01 A:8-292                                                                                                                                                                                                                                                                        ----------------- Pfam domains
         Sec.struct. author ........ee.eee..hhhhhhhhhhhhhhhhhh..ee...ee.hhhhhhhhhhh....eeeeeee..hhhhhhhhhhhh.ee.....eeee.eeeeeehhhhhhhh..hhhhhhhhhhhhhhh......eeee.....hhhhhhhhhhhhhh.....eeee..hhhhhhhhhhhhhhh....eeeee...hhhhhh.....eee............................eeeeeeeehhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1r9q A   1 ADLPGKGITVNPVQSTITEETFQTLLVSRALEKLGYTVNKPSEVDYNVGYTSLASGDATFTAVNWTPLHDNMYEAAGGDKKFYREGVFVNGAAQGYLIDKKTADQYKITNIAQLKDPKIAKLFDTNGDGKADLTGCNPGWGCEGAINHQLAAYELTNTVTHNQGNYAAMMADTISRYKEGKPVFYYTWTPYWVSNELKPGKDVVWLQVPFSALPGDKNADTKLPNGANYGFPVSTMHIVANKAWAEKNPAAAKLFAIMQLPVADINAQNAIMHDGKASEGDIQGHVDGWIKAHQQQFDGWVNEALAAQK 309
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300         


Chain A from PDB  Type:PROTEIN  Length:309
 aligned with PROX_ECOLI | P0AFM2 from UniProtKB/Swiss-Prot  Length:330

    Alignment length:309
                                    31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321         
           PROX_ECOLI    22 ADLPGKGITVNPVQSTITEETFQTLLVSRALEKLGYTVNKPSEVDYNVGYTSLASGDATFTAVNWTPLHDNMYEAAGGDKKFYREGVFVNGAAQGYLIDKKTADQYKITNIAQLKDPKIAKLFDTNGDGKADLTGCNPGWGCEGAINHQLAAYELTNTVTHNQGNYAAMMADTISRYKEGKPVFYYTWTPYWVSNELKPGKDVVWLQVPFSALPGDKNADTKLPNGANYGFPVSTMHIVANKAWAEKNPAAAKLFAIMQLPVADINAQNAIMHDGKASEGDIQGHVDGWIKAHQQQFDGWVNEALAAQK 330
               SCOP domains d1r9qa_ A: Glycine betaine-binding periplasmic protein ProX                                                                                                                                                                                                                                                           SCOP domains
               CATH domains 1r9qA01 A:1-91,A:233-309 Periplasmic binding protein-like II                               1r9qA02 A:92-232 Glycine betaine-binding periplasmic protein; domain 2                                                                       1r9qA01 A:1-91,A:233-309 Periplasmic binding protein-like II                  CATH domains
               Pfam domains -------OpuAC-1r9qA01 A:8-292                                                                                                                                                                                                                                                                        ----------------- Pfam domains
         Sec.struct. author ........ee.eee..hhhhhhhhhhhhhhhhhh..ee...ee.hhhhhhhhhhh....eeeeeee..hhhhhhhhhhhh.ee.....eeee.eeeeeehhhhhhhh..hhhhhhhhhhhhhhh......eeee.....hhhhhhhhhhhhhh.....eeee..hhhhhhhhhhhhhhh....eeeee...hhhhhh.....eee............................eeeeeeeehhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1r9q A   1 ADLPGKGITVNPVQSTITEETFQTLLVSRALEKLGYTVNKPSEVDYNVGYTSLASGDATFTAVNWTPLHDNMYEAAGGDKKFYREGVFVNGAAQGYLIDKKTADQYKITNIAQLKDPKIAKLFDTNGDGKADLTGCNPGWGCEGAINHQLAAYELTNTVTHNQGNYAAMMADTISRYKEGKPVFYYTWTPYWVSNELKPGKDVVWLQVPFSALPGDKNADTKLPNGANYGFPVSTMHIVANKAWAEKNPAAAKLFAIMQLPVADINAQNAIMHDGKASEGDIQGHVDGWIKAHQQQFDGWVNEALAAQK 309
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300
   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  (5, 9)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (PROX_ECO57 | P0AFM3)
molecular function
    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:0006865    amino acid transport    The directed movement of amino acids, organic acids containing one or more amino substituents, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
    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.
cellular component
    GO:0042597    periplasmic space    The region between the inner (cytoplasmic) and outer membrane (Gram-negative Bacteria) or cytoplasmic membrane and cell wall (Fungi and Gram-positive Bacteria).

Chain A   (PROX_ECOLI | P0AFM2)
molecular function
    GO:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
    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:0006865    amino acid transport    The directed movement of amino acids, organic acids containing one or more amino substituents, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
    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.
cellular component
    GO:0042597    periplasmic space    The region between the inner (cytoplasmic) and outer membrane (Gram-negative Bacteria) or cytoplasmic membrane and cell wall (Fungi and Gram-positive Bacteria).

 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
    PBE  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    UNX  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Thr A:189 - Pro A:190   [ RasMol ]  
    Thr A:66 - Pro A:67   [ RasMol ]  
 

(-) 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
  1r9q
    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
  PROX_ECO57 | P0AFM3
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
  PROX_ECOLI | P0AFM2
    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
  PROX_ECO57 | P0AFM3
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)
  PROX_ECOLI | P0AFM2
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        PROX_ECO57 | P0AFM3: 1r9l
        PROX_ECOLI | P0AFM2: 1r9l

(-) Related Entries Specified in the PDB File

1r9l PROX IN COMPLEX WITH GLYCINE BETAINE