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

(-) Description

Title :  PCPR INDUCER BINDING DOMAIN (APO-FORM)
 
Authors :  R. P. Hayes, T. W. Moural, K. M. Lewis, D. Onofrei, L. Xun, C. Kang
Date :  25 Oct 14  (Deposition) - 26 Nov 14  (Release) - 26 Nov 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.70
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
Keywords :  Lysr Family Transcriptional Regulator, Transcription (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  R. P. Hayes, T. W. Moural, K. M. Lewis, D. Onofrei, L. Xun, C. Kang
Structures Of The Inducer-Binding Domain Of Pentachlorophenol-Degrading Gene Regulator Pcpr From Sphingobium Chlorophenolicum.
Int J Mol Sci V. 15 20736 2014
PubMed-ID: 25397598  |  Reference-DOI: 10.3390/IJMS151120736

(-) Compounds

Molecule 1 - PCP DEGRADATION TRANSCRIPTIONAL ACTIVATION PROTEIN
    Chains: A, B, C, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: RESIDUES 85-307
    Gene: PCPR
    Organism Scientific: SPHINGOBIUM CHLOROPHENOLICUM
    Organism Taxid: 46429

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): AB  
Biological Unit 2 (1x):   CD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 4RNS)

(-) Sites  (0, 0)

(no "Site" information available for 4RNS)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4RNS)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4RNS)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4RNS)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4RNS)

(-) Exons   (0, 0)

(no "Exon" information available for 4RNS)

(-) 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:214
                                                                                                                                                                                                                                                      
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........eeeee.hhhhhhhhh..hhhhhhhhh...eeeee.....hhhhhhhh....eeee........eeeeeeeee.eeeeee..hhhhh...hhhhhhhh.eeee.hhhhhhhhhhhhhhhhhhhhhh.eeeee.hhhhhhhhhhhh...eeeehhhhhhhhh...eeee........eeeeeeee.hhh.hhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4rns A  89 RFDPGTSNRNFRIAASDFGQALMLPRLYATLEETAPQVRVTGVNLRHGPLVEELESGSIDIAFGGFPTLSAGIKTQTLFREEYVCVMRQSHPALTHGLDLEAFRQCRHIIVTAHEFNHVHEQVEARLLELLPPESIRFTTENFLVSAVIAEETDVILTIPSRLARWFANRGGLTIFPVPIELPSIEVKQYWHERYDKDPGNIWLRRVIAKIGFQ 302
                                    98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298    


Chain B from PDB  Type:PROTEIN  Length:213
                                                                                                                                                                                                                                                     
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........eeeee.hhhhhhhhh..hhhhhhhhh...eeeee.....hhhhhhhhh...eeee........eeeeeeeee.eeeeee....hhhhh.hhhhhhh.eeeee.hhhhhhhhhhhhhhhhhhh....eeeee.hhhhhhhhhhhh.eeeeeehhhhhhhhhh..eeee........eeeeeeee.hhh.hhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4rns B  90 FDPGTSNRNFRIAASDFGQALMLPRLYATLEETAPQVRVTGVNLRHGPLVEELESGSIDIAFGGFPTLSAGIKTQTLFREEYVCVMRQSHPALTHGLDLEAFRQCRHIIVTAHEFNHVHEQVEARLLELLPPESIRFTTENFLVSAVIAEETDVILTIPSRLARWFANRGGLTIFPVPIELPSIEVKQYWHERYDKDPGNIWLRRVIAKIGFQ 302
                                    99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299   


Chain C from PDB  Type:PROTEIN  Length:217
                                                                                                                                                                                                                                                         
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........eeeee.hhhhhhhhhhhhhhhhhhhh...eeeee.....hhhhhhhhh...eeee........eeeeeeeee.eeeeee..hhhhh...hhhhhhhheeeee.hhhhhhhhhhhhhhhhhhhhhh.eeeee.hhhhhhhhhhhh.eeeeeehhhhhhhhhhh.eeee........eeeeeeee.hhh.hhhhhhhhhhhhh........ Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4rns C  90 FDPGTSNRNFRIAASDFGQALMLPRLYATLEETAPQVRVTGVNLRHGPLVEELESGSIDIAFGGFPTLSAGIKTQTLFREEYVCVMRQSHPALTHGLDLEAFRQCRHIIVTAHEFNHVHEQVEARLLELLPPESIRFTTENFLVSAVIAEETDVILTIPSRLARWFANRGGLTIFPVPIELPSIEVKQYWHERYDKDPGNIWLRRVIAKIGFQNPPA 306
                                    99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       


Chain D from PDB  Type:PROTEIN  Length:217
                                                                                                                                                                                                                                                         
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........eeeee.hhhhhhhhhhhhhhhhhhhh...eeeee.....hhhhhhhh....eeee........eeeeeeeee.eeeeee..hhhhh...hhhhhhh.eeeee.hhhhhhhhhhhhhhhhhhhhhh.eeeee.hhhhhhhhhhhh.eeeeeehhhhhhhhh...eeeee.......eeeeeeee.hhh.hhhhhhhhhhhhh........ Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4rns D  90 FDPGTSNRNFRIAASDFGQALMLPRLYATLEETAPQVRVTGVNLRHGPLVEELESGSIDIAFGGFPTLSAGIKTQTLFREEYVCVMRQSHPALTHGLDLEAFRQCRHIIVTAHEFNHVHEQVEARLLELLPPESIRFTTENFLVSAVIAEETDVILTIPSRLARWFANRGGLTIFPVPIELPSIEVKQYWHERYDKDPGNIWLRRVIAKIGFQNPPA 306
                                    99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299
   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 4RNS)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4RNS)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4RNS)

(-) Gene Ontology  (5, 5)

Asymmetric Unit(hide GO term definitions)

 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
(no "Ligands, Modified Residues, Ions" information available for 4rns)
 
  Sites
(no "Sites" information available for 4rns)
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 4rns)
 
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 | Biol. Unit 1 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
  4rns
    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
  PCPR_SPHCR | P52679
    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
  PCPR_SPHCR | P52679
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        PCPR_SPHCR | P52679: 4rpn 4rpo

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 4RNS)