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

(-) Description

Title :  TREHALOSE REPRESSOR FROM ESCHERICHIA COLI
 
Authors :  U. Hars, R. Horlacher, W. Boos, O. S. Smart, G. Bricogne, W. Welte, K. Die
Date :  30 Jan 15  (Deposition) - 11 Feb 15  (Release) - 10 Jun 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.40
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Laci Family, Phosphate Binding, Protein Structure, Trehalose Repressor, Gene Regulation (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  U. Hars, R. Horlacher, W. Boos, W. Welte, K. Diederichs
Crystal Structure Of The Effector-Binding Domain Of The Trehalose-Repressor Of Escherichia Coli, A Member Of The Laci Family, In Its Complexes With Inducer Trehalose-6-Phosphate And Noninducer Trehalose.
Protein Sci. V. 7 2511 1998
PubMed-ID: 9865945  |  Reference-DOI: 10.1002/PRO.5560071204
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - HTH-TYPE TRANSCRIPTIONAL REGULATOR TRER
    Chains: A, B
    Fragment: EFFECTOR BINDING DOMAIN, UNP RESIDUES 61-315
    Organism Scientific: ESCHERICHIA COLI K-12
    Organism Taxid: 83333
    Synonym: TREHALOSE OPERON REPRESSOR

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric/Biological Unit (1, 2)
No.NameCountTypeFull Name
1T6P2Ligand/IonTREHALOSE-6-PHOSPHATE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:71 , SER A:74 , LEU A:75 , SER A:76 , GLU A:77 , PHE A:125 , GLY A:126 , ARG A:147 , ASP A:187 , THR A:190 , ARG A:194 , THR A:240 , THR A:242 , TYR A:284 , HOH A:513 , HOH A:514 , HOH A:523 , HOH A:524 , HOH A:532 , HOH A:539binding site for residue T6P A 401
2AC2SOFTWAREARG B:71 , SER B:74 , LEU B:75 , SER B:76 , GLU B:77 , PHE B:125 , GLY B:126 , ARG B:147 , ASP B:187 , THR B:189 , THR B:190 , ARG B:194 , THR B:240 , THR B:242 , TYR B:284 , HOH B:515 , HOH B:516 , HOH B:521 , HOH B:522 , HOH B:528binding site for residue T6P B 401

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4XXH)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4XXH)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4XXH)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4XXH)

(-) Exons   (0, 0)

(no "Exon" information available for 4XXH)

(-) 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:255
                                                                                                                                                                                                                                                                                               
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeee....hhhhhhhhhhhhhhhhhhh.eeeeee...hhhhhhhhhhhhhhh...eeeee.........hhhhh..eeee.......eeeeehhhhhhhhhhhhhhhh....eeee.........hhhhhhhhhhhhhhh....eee....hhhhhhhhhhhhh.....eeee.hhhhhhhhhhhhhhh.....eeeee..hhhhhhhh...eeee.hhhhhhhhhhhhhhhhhh......eeee..ee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4xxh A  61 SDKVVAIIVTRLDSLSENLAVQTMLPAFYEQGYDPIMMESQFSPQLVAEHLGVLKRRNIDGVVLFGFTGITEEMLAHWQSSLVLLARDAKGFASVCYDDEGAIKILMQRLYDQGHRNISYLGVPHSDVTTGKRRHEAYLAFCKAHKLHPVAALPGLAMKQGYENVAKVITPETTALLCATDTLALGASKYLQEQRIDTLQLASVGNTPLMKFLHPEIVTVDPGYAEAGRQAACQLIAQVTGRSEPQQIIIPATLS 315
                                    70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310     


Chain B from PDB  Type:PROTEIN  Length:255
                                                                                                                                                                                                                                                                                               
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeee....hhhhhhhhhhhhhhhhhhh.eeeeee...hhhhhhhhhhhhhhh...eeeee......hhhhhhhh..eeee.......eeeeehhhhhhhhhhhhhhhh....eeee.........hhhhhhhhhhhhhhh.....ee....hhhhhhhhhhhhh.....eeee.hhhhhhhhhhhhhhh.....eeeee..hhhhhhhh...eeee.hhhhhhhhhhhhhhhhhh......eeee..ee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4xxh B  61 SDKVVAIIVTRLDSLSENLAVQTMLPAFYEQGYDPIMMESQFSPQLVAEHLGVLKRRNIDGVVLFGFTGITEEMLAHWQSSLVLLARDAKGFASVCYDDEGAIKILMQRLYDQGHRNISYLGVPHSDVTTGKRRHEAYLAFCKAHKLHPVAALPGLAMKQGYENVAKVITPETTALLCATDTLALGASKYLQEQRIDTLQLASVGNTPLMKFLHPEIVTVDPGYAEAGRQAACQLIAQVTGRSEPQQIIIPATLS 315
                                    70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310
   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  (0, 0 ; only for superseded entry 1BYK: 1,2)

(no "SCOP Domain" information available for 4XXH, only for superseded entry 1BYK replaced by 4XXH)

(-) CATH Domains  (0, 0 ; only for superseded entry 1BYK: 1,4)

(no "CATH Domain" information available for 4XXH, only for superseded entry 1BYK replaced by 4XXH)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4XXH)

(-) Gene Ontology  (6, 6)

Asymmetric/Biological Unit(hide GO term definitions)

 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
    T6P  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 4xxh)
 

(-) 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
  4xxh
    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
  TRER_ECOLI | P36673
    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
  TRER_ECOLI | P36673
    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 4XXH)

(-) Related Entries Specified in the PDB File

1byk THIS ENTRY REPRESENTS A RE-REFINEMENT OF PDB ENTRY 1BYK USING A NEW SET OF STRUCTURE FACTORS OBTAINED BY RE-PROCESSING THE ORIGINAL IMAGES. THE STEREOCHEMISTRY FOR THE TREHALOSE-6-PHOSPHATE LIGAND HAS BEEN CORRECTED