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 :  CRYSTAL STRUCTURE OF PUTATIVE TRANSCRIPTION REGULATION REPRESSOR (LACI FAMILY) FROM CORYNEBACTERIUM GLUTAMICUM
 
Authors :  Y. Patskovsky, U. Ramagopal, R. Toro, R. Foti, J. Freeman, J. Do, J. M. Sa S. K. Burley, S. C. Almo, New York Sgx Research Center For Struct Genomics (Nysgxrc)
Date :  16 Sep 09  (Deposition) - 22 Sep 09  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Structural Genomics, Psi-2, Sugar Binding Protein, Transcription Regulation, Protein Structure Initiative, New York Sgx Research Center For Structural Genomics, Nysgxrc, Dna-Binding, Transcription, Uncharacterized Protein, Transcription Regulator (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Y. Patskovsky, U. Ramagopal, R. Toro, R. Foti, J. Freeman, J. Do, J. M. Sauder, S. K. Burley, S. C. Almo
Crystal Structure Of Laci Family Protein From Corynebacterium Glutamicum
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - TRANSCRIPTIONAL REGULATORS
    Atcc: 13032
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: MODIFIED PET26
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: CGL2044, YCZA
    Organism Scientific: CORYNEBACTERIUM GLUTAMICUM
    Organism Taxid: 1718
    Synonym: LACI FAMILY PROTEIN

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 4)

Asymmetric/Biological Unit (2, 4)
No.NameCountTypeFull Name
1GOL1Ligand/IonGLYCEROL
2SO43Ligand/IonSULFATE ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:248 , SER B:273 , ARG B:320BINDING SITE FOR RESIDUE SO4 A 334
2AC2SOFTWARESER A:273 , ARG A:320 , ARG B:248BINDING SITE FOR RESIDUE SO4 A 335
3AC3SOFTWAREARG A:256 , HOH A:379BINDING SITE FOR RESIDUE SO4 A 336
4AC4SOFTWAREHIS B:210 , PHE B:211BINDING SITE FOR RESIDUE GOL B 334

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Val A:257 -Pro A:258
2Val B:257 -Pro B:258

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3JVD)

(-) 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
 aligned with Q8NNY3_CORGL | Q8NNY3 from UniProtKB/TrEMBL  Length:325

    Alignment length:262
                                    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  
         Q8NNY3_CORGL    62 SALVGVIVPDLSNEYYSESLQTIQQDLKAAGYQMLVAEANSVQAQDVVMESLISIQAAGIIHVPVVGSIAPEGIPMVQLTRGELGPGFPRVLCDDEAGFFQLTESVLGGSGMNIAALVGEESLSTTQERMRGISHAASIYGAEVTFHFGHYSVESGEEMAQVVFNNGLPDALIVASPRLMAGVMRAFTRLNVRVPHDVVIGGYDDPEWYSFVGAGITTFVPPHEEMGKEAVRLLVDLIENPELPTGDVVLQGQVILRGSSTH 323
               SCOP domains d3jvda_ A: automated matches                                                                                                                                                                                                                                           SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee....hhhhhhhhhhhhhhhhhhh.eeeeee..hhhhhhhhhhhhhhhh..eeee........-....eeee..----....eeeehhhhhhhhhhhhhh.....eeeeee....hhhhhhhhhhhhhhhhhh..eeeeee...hhhhhhhhhhhhhhh....eeee.hhhhhhhhhhhhhhh........eeeee..hhhhhhh....eeee.hhhhhhhhhhhhhhhhhhh..--...eee..eee.hhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3jvd A  64 SALVGVIVPDLSNEYYSESLQTIQQDLKAAGYQMLVAEANSVQAQDVVMESLISIQAAGIIHVPVVGSIA-EGIPMVQLTR----PGFPRVLCDDEAGFFQLTESVLGGSGMNIAALVGEESLSTTQERMRGISHAASIYGAEVTFHFGHYSVESGEEMAQVVFNNGLPDALIVASPRLMAGVMRAFTRLNVRVPHDVVIGGYDDPEWYSFVGAGITTFVPPHEEMGKEAVRLLVDLIENPE--TGDVVLQGQVILRGSSTH 325
                                    73        83        93       103       113       123       133 |     143|    | 153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303 |  |  313       323  
                                                                                               133 |      144  149                                                                                                                                                         305  |                 
                                                                                                 135                                                                                                                                                                          308                 


Chain B from PDB  Type:PROTEIN  Length:258
 aligned with Q8NNY3_CORGL | Q8NNY3 from UniProtKB/TrEMBL  Length:325

    Alignment length:262
                                    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  
         Q8NNY3_CORGL    62 SALVGVIVPDLSNEYYSESLQTIQQDLKAAGYQMLVAEANSVQAQDVVMESLISIQAAGIIHVPVVGSIAPEGIPMVQLTRGELGPGFPRVLCDDEAGFFQLTESVLGGSGMNIAALVGEESLSTTQERMRGISHAASIYGAEVTFHFGHYSVESGEEMAQVVFNNGLPDALIVASPRLMAGVMRAFTRLNVRVPHDVVIGGYDDPEWYSFVGAGITTFVPPHEEMGKEAVRLLVDLIENPELPTGDVVLQGQVILRGSSTH 323
               SCOP domains d3jvdb_ B: automated matches                                                                                                                                                                                                                                           SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee....hhhhhhhhhhhhhhhhhh..eeeeee..hhhhhhhhhhhhhhh...eeee...----......eeee..........eeeehhhhhhhhhhhhhh.....eeeeee....hhhhhhhhhhhhhhhhhh..eeeeee...hhhhhhhhhhhhhhh....eeee.hhhhhhhhhhhhhhh........eeeee..hhhhhh.....eeee.hhhhhhhhhhhhhhhhhhh.......eee..eee.hhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3jvd B  64 SALVGVIVPDLSNEYYSESLQTIQQDLKAAGYQMLVAEANSVQAQDVVMESLISIQAAGIIHVPV----APEGIPMVQLTRGELGPGFPRVLCDDEAGFFQLTESVLGGSGMNIAALVGEESLSTTQERMRGISHAASIYGAEVTFHFGHYSVESGEEMAQVVFNNGLPDALIVASPRLMAGVMRAFTRLNVRVPHDVVIGGYDDPEWYSFVGAGITTFVPPHEEMGKEAVRLLVDLIENPELPTGDVVLQGQVILRGSSTH 325
                                    73        83        93       103       113       123    |  133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323  
                                                                                          128  133
   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, 2)

Asymmetric/Biological Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3JVD)

(-) Gene Ontology  (4, 4)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (Q8NNY3_CORGL | Q8NNY3)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0003700    transcription factor activity, sequence-specific DNA binding    Interacting selectively and non-covalently with a specific DNA sequence in order to modulate transcription. The transcription factor may or may not also interact selectively with a protein or macromolecular complex.
biological process
    GO:0006355    regulation of transcription, DNA-templated    Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
    GO:0006351    transcription, DNA-templated    The cellular synthesis of RNA on a template of DNA.

 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
    GOL  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    SO4  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
    AC4  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Val A:257 - Pro A:258   [ RasMol ]  
    Val B:257 - Pro B:258   [ 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
  3jvd
    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
  Q8NNY3_CORGL | Q8NNY3
    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
  Q8NNY3_CORGL | Q8NNY3
    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 3JVD)

(-) Related Entries Specified in the PDB File

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