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 :  ROK REPRESSOR LMO0178 FROM LISTERIA MONOCYTOGENES BOUND TO INDUCER
 
Authors :  S. H. Light, W. F. Anderson, Center For Structural Genomics Of Inf Diseases (Csgid)
Date :  08 Dec 15  (Deposition) - 07 Sep 16  (Release) - 23 Nov 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.85
Chains :  Asym./Biol. Unit :  A,E
Keywords :  Repressor, Open Reading Frame, Kinase, Structural Genomics, Psi- Biology, Center For Structural Genomics Of Infectious Diseases, Csgid, Transcription (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. H. Light, L. A. Cahoon, A. S. Halavaty, N. E. Freitag, W. F. Anderson
Structure To Function Of An Alpha-Glucan Metabolic Pathway That Promotes Listeria Monocytogenes Pathogenesis.
Nat Microbiol V. 2 16202 2016
PubMed-ID: 27819654  |  Reference-DOI: 10.1038/NMICROBIOL.2016.202

(-) Compounds

Molecule 1 - LMO0178 PROTEIN
    Chains: E, A
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21
    Expression System Taxid: 511693
    Gene: LMO0178
    Organism Scientific: LISTERIA MONOCYTOGENES SEROVAR 1/2A (STRAIN ATCC BAA-679 / EGD-E)
    Organism Taxid: 169963
    Strain: ATCC BAA-679 / EGD-E
    Synonym: ROK REPRESSOR

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AE

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 9)

Asymmetric/Biological Unit (5, 9)
No.NameCountTypeFull Name
1CL1Ligand/IonCHLORIDE ION
2GLC4Ligand/IonALPHA-D-GLUCOSE
3PEG1Ligand/IonDI(HYDROXYETHYL)ETHER
4PO41Ligand/IonPHOSPHATE ION
5ZN2Ligand/IonZINC ION

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS E:244 , CYS E:254 , CYS E:256 , CYS E:261binding site for residue ZN E 503
2AC2SOFTWARELYS A:259 , ARG E:322binding site for residue CL E 504
3AC3SOFTWARETYR A:319 , ARG A:322 , GLN E:258 , LYS E:259 , HOH E:612 , HOH E:617 , HOH E:680binding site for residue PO4 E 505
4AC4SOFTWAREHIS A:244 , CYS A:254 , CYS A:256 , CYS A:261binding site for residue ZN A 503
5AC5SOFTWAREASN A:329 , PRO A:330 , PHE A:359 , PHE A:364 , THR A:366 , GLN E:236binding site for residue PEG A 504
6AC6SOFTWARELYS A:89 , GLU A:91 , GLU A:92 , GLY A:152 , LYS A:191 , ASN A:192 , SER A:216 , VAL A:217 , GLY A:218 , GLY A:220 , LEU A:221 , GLY A:222 , GLU A:241 , HIS A:244 , GLU A:263 , GLU A:338 , TRP A:378 , HOH A:610 , HOH A:654 , HOH A:662 , HOH A:672 , HOH A:678binding site for Poly-Saccharide residues GLC A 501 through GLC A 502
7AC7SOFTWARELYS E:89 , GLU E:91 , GLU E:92 , SER E:151 , GLY E:152 , LYS E:191 , ASN E:192 , SER E:216 , VAL E:217 , GLY E:218 , GLY E:220 , LEU E:221 , GLY E:222 , GLU E:241 , HIS E:244 , GLU E:263 , GLU E:338 , TRP E:378 , HOH E:616 , HOH E:657 , HOH E:661 , HOH E:677binding site for Poly-Saccharide residues GLC E 501 through GLC E 502

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5F7R)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 5F7R)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5F7R)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5F7R)

(-) Exons   (0, 0)

(no "Exon" information available for 5F7R)

(-) 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:306
                                                                                                                                                                                                                                                                                                                                                  
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeeeee...eeeeeee.....eeeeeeee.....hhhhhhhhhhhhhhhhhh..hhh.eeeeeeee..eee....eeeee....eeeehhhhhhhhhh....eeeeehhhhhhhhhhhhh......eeeeee.....eeeeee..ee.........hhhhh...............hhhhh..hhhhhhhhhhhh........hhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhh..eeeeehhhhhhhhhhhhhhhhhhh...hhhhh...eeee.....hhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5f7r A  83 GFVVSVKVEEEQLLFALTDLNAEIIENTSIPFSSEKKPEEAIELIAKNVKKMCGNRDMNHLLGVGIAISGLVNRKKGTVIRSTMLGWENVALEAMLHAHFPDIPVYVDKNINCYTLAELWLGEGKQSNNFATVSVGAGLGLSVVINRQIYYGAQGGAGEFGHTTIQPGGYKCHCGQKGCLEMYASEFYFRNRGEELKEAYPLNDFHFDKVAKSARAGDEMATELMGKMGEYLGYGIRNIINTFNPEKVIIVGEGLHHRDLFLTKIDEIASQNFFSGAGFETEITTTSLEDPAWLQGAALLVIHQLF 391
                                    92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282||     295       305       315       325       335       345       355       365       375       385      
                                                                                                                                                                                                                                  283|                                                                                                        
                                                                                                                                                                                                                                   287                                                                                                        


Chain E from PDB  Type:PROTEIN  Length:304
                                                                                                                                                                                                                                                                                                                                                
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeee...eeeeeee.....eeeeeeee.....hhhhhhhhhhhhhhhhh..eeeeeeee..eee....eeeee....eeeehhhhhhhhhh....eeeeehhhhhhhhhhhhh......eeeeee.....eeeeee..ee.........hhhhh...............hhhhh..hhhhhhhhhhhh...........hhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhh..eeeeehhhhhhhhhhhhhhhhhhh...hhhhh...eeee.....hhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5f7r E  83 GFVVSVKVEEEQLLFALTDLNAEIIENTSIPFSSEKKPEEAIELIAKNVKKMCNHLLGVGIAISGLVNRKKGTVIRSTMLGWENVALEAMLHAHFPDIPVYVDKNINCYTLAELWLGEGKQSNNFATVSVGAGLGLSVVINRQIYYGAQGGAGEFGHTTIQPGGYKCHCGQKGCLEMYASEFYFRNRGEELKEAYPTSELNDFHFDKVAKSARAGDEMATELMGKMGEYLGYGIRNIINTFNPEKVIIVGEGLHHRDLFLTKIDEIASQNFFSGAGFETEITTTSLEDPAWLQGAALLVIHQLF 391
                                    92       102       112       122       132  ||   147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357       367       377       387    
                                                                              135|                                                                                                                                                                                                                                                          
                                                                               141
   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)

(no "SCOP Domain" information available for 5F7R)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5F7R)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5F7R)

(-) Gene Ontology  (0, 0)

Asymmetric/Biological Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 5F7R)

 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
    CL  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    GLC  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    PEG  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    PO4  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    ZN  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
    AC4  [ RasMol ]  +environment [ RasMol ]
    AC5  [ RasMol ]  +environment [ RasMol ]
    AC6  [ RasMol ]  +environment [ RasMol ]
    AC7  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 5f7r)
 

(-) 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
  5f7r
    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
  Q8YAF1_LISMO | Q8YAF1
    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
  Q8YAF1_LISMO | Q8YAF1
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/TrEMBL
        Q8YAF1_LISMO | Q8YAF1: 5f7p 5f7q

(-) Related Entries Specified in the PDB File

5f7p 5f7q 5f7v