Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asymmetric Unit
(-)Asym. Unit - sites
(-)Biological Unit 1
(-)Biol. Unit 1 - sites
collapse expand < >
Image Asymmetric Unit
Asymmetric Unit  (Jmol Viewer)
Image Asym. Unit - sites
Asym. Unit - sites  (Jmol Viewer)
Image Biological Unit 1
Biological Unit 1  (Jmol Viewer)
Image Biol. Unit 1 - sites
Biol. Unit 1 - sites  (Jmol Viewer)

(-) Description

Title :  THE CRYSTAL STRUCTURE OF THE N-TERMINAL DOMAIN OF A MERR-LIKE TRANSCRIPTIONAL REGULATOR FROM LISTERIA MONOCYTOGENES EGD-E
 
Authors :  K. Tan, M. Gu, S. Peterson, W. F. Anderson, A. Joachimiak, Center For S Genomics Of Infectious Diseases (Csgid)
Date :  11 Jan 11  (Deposition) - 26 Jan 11  (Release) - 26 Jan 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.87
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Structural Genomics, The Center For Structural Genomics Of Infectious Diseases, Csgid, Merr Family, Dna-Binding, All-Alpha, Merr/Dna- Binding, Cytoplasmic, Transcription Regulator (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  K. Tan, M. Gu, S. Peterson, W. F. Anderson, A. Joachimiak, Center For Structural Genomics Of Infectious Diseases (Csgid)
The Crystal Structure Of The N-Terminal Domain Of A Merr-Like Transcriptional Regulator From Listeria Monocytogenes Egd-E
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - MERR-LIKE TRANSCRIPTIONAL REGULATOR
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PMCSG7
    Expression System Strain: BL21
    Expression System Taxid: 511693
    Expression System Vector Type: PLASMID
    Gene: LMO0526
    Organism Scientific: LISTERIA MONOCYTOGENES
    Organism Taxid: 169963
    Strain: EGD-E
    Synonym: LMO0526 PROTEIN

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (2x): A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 10)

Asymmetric Unit (2, 10)
No.NameCountTypeFull Name
1GOL6Ligand/IonGLYCEROL
2MSE4Mod. Amino AcidSELENOMETHIONINE
Biological Unit 1 (2, 20)
No.NameCountTypeFull Name
1GOL12Ligand/IonGLYCEROL
2MSE8Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETRP A:33 , LEU A:71 , PHE A:72 , ASP A:73 , VAL A:76 , HOH A:300BINDING SITE FOR RESIDUE GOL A 247
2AC2SOFTWARELEU A:9 , THR A:10 , GLY A:11 , PHE A:118 , PHE A:121 , HOH A:312 , HOH A:322 , HOH A:350BINDING SITE FOR RESIDUE GOL A 248
3AC3SOFTWARETHR A:94 , ALA A:97 , THR A:98 , THR A:119 , HOH A:297BINDING SITE FOR RESIDUE GOL A 249
4AC4SOFTWARELYS A:4 , ASP A:45 , ASN A:105 , GLU A:106 , LYS A:117 , HOH A:268 , HOH A:279BINDING SITE FOR RESIDUE GOL A 250
5AC5SOFTWARELEU A:60 , LYS A:61 , HOH A:310BINDING SITE FOR RESIDUE GOL A 251
6AC6SOFTWAREILE A:3 , TYR A:36 , ARG A:37 , GLY A:108 , GLU A:109 , HOH A:270BINDING SITE FOR RESIDUE GOL A 252

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3QAO)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3QAO)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3QAO)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3QAO)

(-) Exons   (0, 0)

(no "Exon" information available for 3QAO)

(-) Sequences/Alignments

Asymmetric 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:140
 aligned with Q8Y9K1_LISMO | Q8Y9K1 from UniProtKB/TrEMBL  Length:246

    Alignment length:140
                               1                                                                                                                                        
                               |     7        17        27        37        47        57        67        77        87        97       107       117       127       137
         Q8Y9K1_LISMO     - ---MQIKELAELTGVSVRTLHHYDKIGLLVPQKDDWNGYRIYSEKDVDKLQQILFFKELDFPLKKIQQILDDPLFDKNVALDMQRHLLIEKKQRIETMLATLDLTIKNEKGEITMTNKEKFTGFDFSSNPYEEEARKLWG 137
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----MerR-3qaoA01 A:2-39                   ----MerR-DNA-bind-3qaoA02 A:44-104                               ----------------------TipAS-3qaoA Pfam domains
         Sec.struct. author ....hhhhhhhhhh.hhhhhhhhhhh.....ee......ee.hhhhhhhhhhhhhhhhh..hhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhh...........hhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3qao A  -2 SNAmQIKELAELTGVSVRTLHHYDKIGLLVPQKDDWNGYRIYSEKDVDKLQQILFFKELDFPLKKIQQILDDPLFDKNVALDmQRHLLIEKKQRIETmLATLDLTIKNEKGEITmTNKEKFTGFDFSSNPYEEEARKLWG 137
                               |     7        17        27        37        47        57        67        77  |     87       |97       107    |  117       127       137
                               |                                                                             80-MSE         95-MSE          112-MSE                     
                               1-MSE
   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 3QAO)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3QAO)

(-) Pfam Domains  (3, 3)

Asymmetric Unit
(-)
Clan: HTH (544)
(-)
Clan: no clan defined [family: TipAS] (2)

(-) Gene Ontology  (2, 2)

Asymmetric Unit(hide GO term definitions)
Chain A   (Q8Y9K1_LISMO | Q8Y9K1)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
biological process
    GO:0006355    regulation of transcription, DNA-templated    Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.

 Visualization

(-) Interactive Views

Asymmetric 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
    GOL  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    MSE  [ 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 ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 3qao)
 
Biological Unit
  Complete Structure
    Biological Unit 1  [ Jena3D ]

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym. Unit PNG format | Asym. Unit - sites PNG format | Biol. Unit 1 PNG format | Biol. Unit 1 - 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
  3qao
    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
  Q8Y9K1_LISMO | Q8Y9K1
    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
  Q8Y9K1_LISMO | Q8Y9K1
    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 3QAO)

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 3QAO)