Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Biol.Unit 2 - manually
(-)Asymmetric Unit
(-)Asym. Unit - sites
(-)Biological Unit 1
(-)Biol. Unit 1 - sites
(-)Biological Unit 2
collapse expand < >
Image Biol.Unit 2 - manually
Biol.Unit 2 - manually  (Jmol Viewer)
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)
Image Biological Unit 2
Biological Unit 2  (Jmol Viewer)

(-) Description

Title :  CRYSTAL STRUCTURE OF LACI FAMILY TRANSCRIPTION REGULATOR FROM CLOSTRIDIUM ACETOBUTYLICUM
 
Authors :  A. Bagaria, S. K. Burley, S. Swaminathan, New York Sgx Research Cen Structural Genomics (Nysgxrc)
Date :  11 Feb 09  (Deposition) - 24 Feb 09  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.84
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  A  (2x)
Keywords :  Transcription Regulator, Psi-Ii, 11230O, Structural Genomics, Protein Structure Initiative, New York Sgx Research Center For Structural Genomics, Nysgxrc, New York Structural Genomix Research Consortium, Dna-Binding, Transcription, Transcription Regulation (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. Bagaria, S. K. Burley, S. Swaminathan
Crystal Structure Of Laci Family Transcription Regulator From Clostridium Acetobutylicum
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - TRANSCRIPTIONAL REGULATOR (LACI FAMILY)
    Atcc: 824
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PSGX3(BC)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 58-335
    Gene: CA_C3553
    Organism Scientific: CLOSTRIDIUM ACETOBUTYLICUM ATCC 824
    Organism Taxid: 272562
    Strain: DSM 792 / JCM 1419 / LMG 5710 / VKM B-1787

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 6)

Asymmetric Unit (2, 6)
No.NameCountTypeFull Name
1GOL1Ligand/IonGLYCEROL
2MSE5Mod. Amino AcidSELENOMETHIONINE
Biological Unit 1 (2, 6)
No.NameCountTypeFull Name
1GOL1Ligand/IonGLYCEROL
2MSE5Mod. Amino AcidSELENOMETHIONINE
Biological Unit 2 (2, 12)
No.NameCountTypeFull Name
1GOL2Ligand/IonGLYCEROL
2MSE10Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASN A:152 , MSE A:196 , ARG A:199BINDING SITE FOR RESIDUE GOL A 401

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3G85)

(-) Cis Peptide Bonds  (3, 3)

Asymmetric Unit
No.Residues
1Ile A:268 -Pro A:269
2Thr A:289 -Pro A:290
3Asn A:320 -Pro A:321

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3G85)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3G85)

(-) Exons   (0, 0)

(no "Exon" information available for 3G85)

(-) 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:270
 aligned with Q97DC5_CLOAB | Q97DC5 from UniProtKB/TrEMBL  Length:335

    Alignment length:270
                                    74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334
         Q97DC5_CLOAB    65 KPTIALYWSSDISVNIISRFLRGLQSKLAKQNYNYNVVICPYKTDCLHLEKGISKENSFDAAIIANISNYDLEYLNKASLTLPIILFNRLSNKYSSVNVDNYKMGEKASLLFAKKRYKSAAAILTESLNDAMDNRNKGFIETCHKNGIKISENHIIAAENSIHGGVDAAKKLMKLKNTPKALFCNSDSIALGVISVLNKRQISIPDDIEIVAIGMNDREYTEFSTPPVTIVDIPIEEMAGTCISLVEKLINRDIENPTSILFDGPLILRN 334
               SCOP domains d3g85a_ A: automated matches                                                                                                                                                                                                                                                   SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeeeeee...hhhhhhhhhhhhhhhhhhh....eeeeeee...hhhhhhhhh......eeee...hhhhhhhhhhh.....eeee.......eeeeehhhhhhhhhhhhhhhh.....eeee....hhhhhhhhhhhhhhhhhh....hhh.eee...hhhhhhhhhhhhh.......eeee.hhhhhhhhhhhhhhh........eeeeee...hhhhhh.....eeee.hhhhhhhhhhhhhhhhhh.......eeee...ee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3g85 A  65 KPTIALYWSSDISVNIISRFLRGLQSKLAKQNYNYNVVICPYKTDCLHLEKGISKENSFDAAIIANISNYDLEYLNKASLTLPIILFNRLSNKYSSVNVDNYKmGEKASLLFAKKRYKSAAAILTESLNDAmDNRNKGFIETCHKNGIKISENHIIAAENSIHGGVDAAKKLmKLKNTPKALFCNSDSIALGVISVLNKRQISIPDDIEIVAIGmNDREYTEFSTPPVTIVDIPIEEmAGTCISLVEKLINRDIENPTSILFDGPLILRN 334
                                    74        84        94       104       114       124       134       144       154       164   |   174       184       194 |     204       214       224       234  |    244       254       264       274    |  284       294       304       314       324       334
                                                                                                                                 168-MSE                     196-MSE                                  237-MSE                                   279-MSE                302-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  (1, 1)

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

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3G85)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3G85)

(-) Gene Ontology  (4, 4)

Asymmetric Unit(hide GO term definitions)
Chain A   (Q97DC5_CLOAB | Q97DC5)
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 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 ]
 
  Cis Peptide Bonds
    Asn A:320 - Pro A:321   [ RasMol ]  
    Ile A:268 - Pro A:269   [ RasMol ]  
    Thr A:289 - Pro A:290   [ RasMol ]  
 
Biological Units
  Complete Structure
    Biological Unit 1  [ Jena3D ]
    Biological Unit 2  [ 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 | Biol. Unit 2 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
  3g85
    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
  Q97DC5_CLOAB | Q97DC5
    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
  Q97DC5_CLOAB | Q97DC5
    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 3G85)

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 3G85)