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 LACI TRANSCRIPTIONAL REGULATOR FROM RHODOCOCCUS SPECIES.
 
Authors :  L. Damodharan, S. K. Burley, S. Swaminathan, New York Sgx Research For Structural Genomics (Nysgxrc)
Date :  15 Oct 09  (Deposition) - 03 Nov 09  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.14
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Psi-Ii, 11026W, Laci Family Protein, Structural Genomics, Protein Structure Initiative, New York Sgx Research Center For Structural Genomics, Nysgxrc, Dna-Binding, Transcription, Transcription Regulation, Transcription Regulator (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  L. Damodhran, S. K. Burley, S. Swaminathan
Crystal Structure Of Laci Transcriptional Regulator From Rhodococcus Species.
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - TRANSCRIPTIONAL REGULATOR, LACI FAMILY PROTEIN
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PSGX3(BC)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: RHA1_RO05266
    Organism Scientific: RHODOCOCCUS JOSTII
    Organism Taxid: 101510
    Strain: RHA1

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 16)

Asymmetric/Biological Unit (2, 16)
No.NameCountTypeFull Name
1GOL2Ligand/IonGLYCEROL
2MSE14Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHOH A:34 , PHE A:84 , ARG A:202 , ASN A:252 , ASP A:280 , GLN A:297BINDING SITE FOR RESIDUE GOL A 349
2AC2SOFTWAREALA B:154 , ARG B:202 , ASN B:252 , ASP B:280 , GLN B:297 , HOH B:387BINDING SITE FOR RESIDUE GOL B 349

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3K9C)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Val A:270 -Pro A:271
2Val B:270 -Pro B:271

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3K9C)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3K9C)

(-) Exons   (0, 0)

(no "Exon" information available for 3K9C)

(-) 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:268
 aligned with Q0S5Y9_RHOJR | Q0S5Y9 from UniProtKB/TrEMBL  Length:341

    Alignment length:268
                                    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       331        
         Q0S5Y9_RHOJR    72 RLLGVVFELQQPFHGDLVEQIYAAATRRGYDVMLSAVAPSRAEKVAVQALMRERCEAAILLGTRFDTDELGALADRVPALVVARASGLPGVGAVRGDDVAGITLAVDHLTELGHRNIAHIDGADAPGGADRRAGFLAAMDRHGLSASATVVTGGTTETEGAEGMHTLLEMPTPPTAVVAFNDRCATGVLDLLVRSGRDVPADISVVGYDDSRLARIPHVQMTTISQDATHMAEAAVDGALAQISGDKAVDLVLAPHLVRRATTGPVAH 339
               SCOP domains d3k9ca_ A: automated matches                                                                                                                                                                                                                                                 SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeee..hhhhhhhhhhhhhhhhhh..eeeeeee....hhhhhhhhhh...eeeeeee....hhhhhhhhhh...eeee.........eeeeehhhhhhhhhhhhhhhh....eeee......hhhhhhhhhhhhhhhhhhhh.eeee....hhhhhhhhhhhhhh......eeee.hhhhhhhhhhhhhhh........eeeeee............eeee.hhhhhhhhhhhhhhhhhhh....eeee..eee.......... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3k9c A  72 RLLGVVFELQQPFHGDLVEQIYAAATRRGYDVmLSAVAPSRAEKVAVQALmRERCEAAILLGTRFDTDELGALADRVPALVVARASGLPGVGAVRGDDVAGITLAVDHLTELGHRNIAHIDGADAPGGADRRAGFLAAmDRHGLSASATVVTGGTTETEGAEGmHTLLEmPTPPTAVVAFNDRCATGVLDLLVRSGRDVPADISVVGYDDSRLARIPHVQmTTISQDATHmAEAAVDGALAQISGDKAVDLVLAPHLVRRATTGPVAH 339
                                    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       331        
                                                          104-MSE           122-MSE                                                                                 210-MSE                  235-MSE |                                                292-MSE   302-MSE                                 
                                                                                                                                                                                                   241-MSE                                                                                              


Chain B from PDB  Type:PROTEIN  Length:271
 aligned with Q0S5Y9_RHOJR | Q0S5Y9 from UniProtKB/TrEMBL  Length:341

    Alignment length:271
                                    77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337 
         Q0S5Y9_RHOJR    68 QASSRLLGVVFELQQPFHGDLVEQIYAAATRRGYDVMLSAVAPSRAEKVAVQALMRERCEAAILLGTRFDTDELGALADRVPALVVARASGLPGVGAVRGDDVAGITLAVDHLTELGHRNIAHIDGADAPGGADRRAGFLAAMDRHGLSASATVVTGGTTETEGAEGMHTLLEMPTPPTAVVAFNDRCATGVLDLLVRSGRDVPADISVVGYDDSRLARIPHVQMTTISQDATHMAEAAVDGALAQISGDKAVDLVLAPHLVRRATTGPVA 338
               SCOP domains d3k9cb_ B: automated matches                                                                                                                                                                                                                                                    SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeeeee..hhhhhhhhhhhhhhhhhh.eeeeeeee....hhhhhhhhhhh..eeeeeee....hhhhhhhhhh...eeee.........eeeeehhhhhhhhhhhhhhhh....eeeee.....hhhhhhhhhhhhhhhh.hhh.eeeee...hhhhhhhhhhhhhhh.....eeee.hhhhhhhhhhhhhhh........eee....hhhhhh......eee.hhhhhhhhhhhhhhhhhh.....eeee..eee......... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3k9c B  68 QASSRLLGVVFELQQPFHGDLVEQIYAAATRRGYDVmLSAVAPSRAEKVAVQALmRERCEAAILLGTRFDTDELGALADRVPALVVARASGLPGVGAVRGDDVAGITLAVDHLTELGHRNIAHIDGADAPGGADRRAGFLAAmDRHGLSASATVVTGGTTETEGAEGmHTLLEmPTPPTAVVAFNDRCATGVLDLLVRSGRDVPADISVVGYDDSRLARIPHVQmTTISQDATHmAEAAVDGALAQISGDKAVDLVLAPHLVRRATTGPVA 338
                                    77        87        97      |107       117    |  127       137       147       157       167       177       187       197       207  |    217       227       237   |   247       257       267       277       287    |  297    |  307       317       327       337 
                                                              104-MSE           122-MSE                                                                                 210-MSE                  235-MSE |                                                292-MSE   302-MSE                                
                                                                                                                                                                                                       241-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, 2)

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

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3K9C)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3K9C)

(-) Gene Ontology  (4, 4)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (Q0S5Y9_RHOJR | Q0S5Y9)
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 ]
    MSE  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Val A:270 - Pro A:271   [ RasMol ]  
    Val B:270 - Pro B:271   [ 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
  3k9c
    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
  Q0S5Y9_RHOJR | Q0S5Y9
    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
  Q0S5Y9_RHOJR | Q0S5Y9
    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 3K9C)

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 3K9C)