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 :  STRUCTURAL GENOMICS, THE CRYSTAL STRUCTURE OF THE C-TERMINAL DOMAIN OF YURK FROM BACILLUS SUBTILIS SUBSP. SUBTILIS STR. 168
 
Authors :  K. Tan, C. Hatzos, J. Abdullah, A. Joachimiak, Midwest Center For Structural Genomics (Mcsg)
Date :  02 Oct 06  (Deposition) - 31 Oct 06  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Apc85442, Yurk, Bacillus Subtilis Subsp. Subtilis Str. 168, Structural Genomics, Psi-2, Protein Structure Initiative, Midwest Center For Structural Genomics, Mcsg, Unknown Function (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  K. Tan, C. Hatzos, J. Abdullah, A. Joachimiak
The Crystal Structure Of The C-Terminal Domain Of Yurk From Bacillus Subtilis Subsp. Subtilis Str. 168
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - HYPOTHETICAL TRANSCRIPTIONAL REGULATOR YURK
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21
    Expression System Plasmid: PMCSG7
    Expression System Strain: BL21
    Expression System Taxid: 511693
    Expression System Vector Type: PLASMID
    Fragment: C-TERMINAL DOMAIN
    Organism Scientific: BACILLUS SUBTILIS
    Organism Taxid: 1423
    Strain: 168

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (2, 6)
No.NameCountTypeFull Name
1MSE4Mod. Amino AcidSELENOMETHIONINE
2SO42Ligand/IonSULFATE ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:132 , VAL A:164 , SER A:165 , MSE A:166 , HIS A:167 , HOH A:296 , HOH A:325BINDING SITE FOR RESIDUE SO4 A 243
2AC2SOFTWAREARG B:132 , VAL B:164 , SER B:165 , MSE B:166 , HIS B:167BINDING SITE FOR RESIDUE SO4 B 243

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2IKK)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Asn B:136 -Asp B:137

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2IKK)

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1HTH_GNTRPS50949 GntR-type HTH domain profile.YURK_BACSU8-76  1A:87-90

(-) Exons   (0, 0)

(no "Exon" information available for 2IKK)

(-) 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:146
 aligned with YURK_BACSU | O32152 from UniProtKB/Swiss-Prot  Length:242

    Alignment length:234
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234    
           YURK_BACSU     5 GSSTPLYIQLKQIITDDIKKGVYSPTAKLPTENELCTKYNVSRITVRKAILDLVEEGYLIRQQGKGTFVKSPKLKRELIAVNGYSEFMESTGKKPKHHVLSHDIIPASKPIAEKLQIQPESPVVELKRILYNDDQPLTFEVTHYPLDLFPGIDTFIADGVSMHDILKQQYKVVPTHNTKLLNVVYAQQEESKYLDCDIGDALFEIDKTAFTSNDQPIYCSLFLMHTNRVTFTIN 238
               SCOP domains ---d 2ikk                                                                                       a1 A:86-238 Hypothetical transcriptional regulator YurK                                                                                    SCOP domains
               CATH domains 2ikk A00                                                                                        A:83-238 Chorismate lyase                                                                                                                  CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..ee-ee..---------------------------------------------------------------------------------------.eeeeeeeee.hhhhhhhhh.....eeeeeeeeee....eeeeeeeeee.....hhhhhh....hhhhhhhhhhh....eeeeeeeeee.hhhhhhhhh.....eeeeeeeeeeehhheeeeeeeeeee...eeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ---HTH_GNTR  PDB: A:87-90 UniProt: 8-76                                 ------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2ikk A  83 GTEN-LYFQ---------------------------------------------------------------------------------------HHVLSHDIIPASKPIAEKLQIQPESPVVELKRILYNDDQPLTFEVTHYPLDLFPGIDTFIADGVSmHDILKQQYKVVPTHNTKLLNVVYAQQEESKYLDCDIGDALFEIDKTAFTSNDQPIYCSLFLmHTNRVTFTIN 238
                               | |  |-         -         -         -         -         -         -         -         -      |104       114       124       134       144       154       164 |     174       184       194       204       214       224   |   234    
                              86 | 90                                                                                     101                                                              166-MSE                                                       228-MSE      
                                87                                                                                                                                                                                                                                    


Chain B from PDB  Type:PROTEIN  Length:145
 aligned with YURK_BACSU | O32152 from UniProtKB/Swiss-Prot  Length:242

    Alignment length:156
                                    93       103       113       123       133       143       153       163       173       183       193       203       213       223       233      
           YURK_BACSU    84 AVNGYSEFMESTGKKPKHHVLSHDIIPASKPIAEKLQIQPESPVVELKRILYNDDQPLTFEVTHYPLDLFPGIDTFIADGVSMHDILKQQYKVVPTHNTKLLNVVYAQQEESKYLDCDIGDALFEIDKTAFTSNDQPIYCSLFLMHTNRVTFTINS 239
               SCOP domains d2ikkb           _ B: automated matches                                                                                                                      SCOP domains
               CATH domains 2ikkB0           0 B:84-239 Chorismate lyase                                                                                                                 CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeee-----------.eeeeeeeee.hhhhhhhhh.....eeeeeeeeee....eeeeeeeeee.....hhhhhh....hhhhhhhhhhh....eeeeeeeeee.hhhhhhhhh.....eeeeeeeeeeehhheeeeeeeeeee....eeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2ikk B  84 TENLYF-----------HHVLSHDIIPASKPIAEKLQIQPESPVVELKRILYNDDQPLTFEVTHYPLDLFPGIDTFIADGVSmHDILKQQYKVVPTHNTKLLNVVYAQQEESKYLDCDIGDALFEIDKTAFTSNDQPIYCSLFLmHTNRVTFTINS 239
                                 |   -       103       113       123       133       143       153       163  |    173       183       193       203       213       223    |  233      
                                89         101                                                              166-MSE                                                       228-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  (2, 2)

Asymmetric/Biological Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2IKK)

(-) Gene Ontology  (4, 4)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (YURK_BACSU | O32152)
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
    MSE  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    SO4  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Asn B:136 - Asp B:137   [ 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
  2ikk
    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
  YURK_BACSU | O32152
    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
  YURK_BACSU | O32152
    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 2IKK)

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 2IKK)