Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asymmetric Unit
(-)Asym. Unit - sites
(-)Biological Unit 1
(-)Biol. Unit 1 - sites
(-)Biological Unit 2
(-)Biological Unit 3
(-)Biological Unit 4
collapse expand < >
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)
Image Biological Unit 3
Biological Unit 3  (Jmol Viewer)
Image Biological Unit 4
Biological Unit 4  (Jmol Viewer)

(-) Description

Title :  CRYSTAL STRUCTURE OF THE UNPHOSPHORYLATED RECEIVER DOMAIN OF DESR IN THE ACTIVE STATE
 
Authors :  F. Trajtenberg, N. Larrieux, A. Buschiazzo
Date :  25 Jun 13  (Deposition) - 16 Jul 14  (Release) - 06 May 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.54
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
Biol. Unit 3:  A (1x),B (1x)
Biol. Unit 4:  C (1x),D (1x)
Keywords :  Response Regulator, Two-Component System, Transcription Factor, Receiver Domain, Dna Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  F. Trajtenberg, D. Albanesi, N. Ruetalo, H. Botti, A. E. Mechaly, M. Nieves, P. S. Aguilar, L. Cybulski, N. Larrieux, D. De Mendoza, A. Buschiazzo
Allosteric Activation Of Bacterial Response Regulators: The Role Of The Cognate Histidine Kinase Beyond Phosphorylation
Mbio V. 5 02105 2014
PubMed-ID: 25406381  |  Reference-DOI: 10.1128/MBIO.02105-14

(-) Compounds

Molecule 1 - TRANSCRIPTIONAL REGULATORY PROTEIN DESR
    Chains: A, B, C, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PQE80L
    Expression System Strain: TOP10F'
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: DESR, YOCG, BSU19200
    Organism Scientific: BACILLUS SUBTILIS SUBSP. SUBTILIS
    Organism Taxid: 224308
    Strain: 168

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): AB  
Biological Unit 2 (1x):   CD
Biological Unit 3 (1x): A (1x)B (1x)  
Biological Unit 4 (1x):   C (1x)D (1x)

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 11)

Asymmetric Unit (2, 11)
No.NameCountTypeFull Name
1K8Ligand/IonPOTASSIUM ION
2PO43Ligand/IonPHOSPHATE ION
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name
1K-1Ligand/IonPOTASSIUM ION
2PO42Ligand/IonPHOSPHATE ION
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1K-1Ligand/IonPOTASSIUM ION
2PO41Ligand/IonPHOSPHATE ION
Biological Unit 3 (1, 1)
No.NameCountTypeFull Name
1K-1Ligand/IonPOTASSIUM ION
2PO41Ligand/IonPHOSPHATE ION
Biological Unit 4 (1, 1)
No.NameCountTypeFull Name
1K-1Ligand/IonPOTASSIUM ION
2PO41Ligand/IonPHOSPHATE ION

(-) Sites  (11, 11)

Asymmetric Unit (11, 11)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREARG A:121 , HOH A:324 , GLU B:108 , PRO B:125 , GLU B:126BINDING SITE FOR RESIDUE PO4 A 201
02AC2SOFTWAREASN A:22 , GLU A:24 , MET A:27BINDING SITE FOR RESIDUE K A 202
03AC3SOFTWAREASP A:54 , GLU A:56 , THR A:81 , ARG A:84 , LYS A:102BINDING SITE FOR RESIDUE K A 203
04AC4SOFTWAREGLU A:108 , LYS B:120 , ARG B:121 , HOH B:327BINDING SITE FOR RESIDUE PO4 B 201
05AC5SOFTWAREASN B:22 , GLU B:24 , MET B:27BINDING SITE FOR RESIDUE K B 202
06AC6SOFTWAREASP B:54 , THR B:81BINDING SITE FOR RESIDUE K B 203
07AC7SOFTWAREGLU C:108 , HOH C:305 , ARG D:121 , HOH D:323BINDING SITE FOR RESIDUE PO4 C 201
08AC8SOFTWAREASN C:22 , GLU C:24 , MET C:27BINDING SITE FOR RESIDUE K C 202
09AC9SOFTWARELYS A:45 , ASP C:49BINDING SITE FOR RESIDUE K C 203
10BC1SOFTWAREASP C:54 , GLU C:56 , THR C:81 , ARG C:84BINDING SITE FOR RESIDUE K C 204
11BC2SOFTWAREASN D:22 , GLU D:24 , MET D:27BINDING SITE FOR RESIDUE K D 201

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4LE2)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4LE2)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4LE2)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4LE2)

(-) Exons   (0, 0)

(no "Exon" information available for 4LE2)

(-) 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:132
                                                                                                                                                                    
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeeee..hhhhhhhhhhhhhh...eeeeeee.hhhhhhhhhhhhh..eeeee......hhhhhhhhh.....eeeeee...hhhhhhhhhhh...eeee....hhhhhhhhhhhhh...eehhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4le2 A   1 MISIFIAEDQQMLLGALGSLLNLEDDMEVVGKGTTGQDAVDFVKKRQPDVCIMDIEMPGKTGLEAAEELKDTGCKIIILTTFARPGYFQRAIKAGVKGYLLKDSPSEELANAIRSVMNGKRIYAPELMEDLY 132
                                    10        20        30        40        50        60        70        80        90       100       110       120       130  


Chain B from PDB  Type:PROTEIN  Length:130
                                                                                                                                                                  
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeee..hhhhhhhhhhhhhh...eeeeeee.hhhhhhhhhhhhh..eeeee......hhhhhhhhh.....eeeeee...hhhhhhhhh...eeee....hhhhhhhhhhhhh...ee.hhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4le2 B  -1 GSMISIFIAEDQQMLLGALGSLLNLEDDMEVVGKGTTGQDAVDFVKKRQPDVCIMDIEMPGKTGLEAAEELKDTGCKIIILTTFPGYFQRAIKAGVKGYLLKDSPSEELANAIRSVMNGKRIYAPELMED 130
                                     8        18        28        38        48        58        68        78   ||   90       100       110       120       130
                                                                                                              82|                                             
                                                                                                               85                                             


Chain C from PDB  Type:PROTEIN  Length:134
                                                                                                                                                                      
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeee..hhhhhhhhhhhhhh...eeeeeee.hhhhhhhhhhhhh..eeeee......hhhhhhhhh.....eeeeee...hhhhhhhhhhh...eeee....hhhhhhhhhhhhh...eehhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4le2 C  -2 SGSMISIFIAEDQQMLLGALGSLLNLEDDMEVVGKGTTGQDAVDFVKKRQPDVCIMDIEMPGKTGLEAAEELKDTGCKIIILTTFARPGYFQRAIKAGVKGYLLKDSPSEELANAIRSVMNGKRIYAPELMEDL 131
                                     7        17        27        37        47        57        67        77        87        97       107       117       127    


Chain D from PDB  Type:PROTEIN  Length:126
                                                                                                                                                              
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeeeee..hhhhhhhhhhhhhh...eeeeeee.hhhhhhhhhhhhh..eeeee......hhhhhhhhh.....eeeeee...hhhhhhh...eeee.....hhhhhhhhhhhh...ee.hhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4le2 D   0 SMISIFIAEDQQMLLGALGSLLNLEDDMEVVGKGTTGQDAVDFVKKRQPDVCIMDIEMPGKTGLEAAEELKDTGCKIIILTTFYFQRAIKAGVKGYLLKDSPSEELANAIRSVMNGKRIYAPELME 129
                                     9        19        29        39        49        59        69        79  ||    93       103       113       123      
                                                                                                             82|                                          
                                                                                                              87
   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 4LE2)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4LE2)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4LE2)

(-) 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
    K  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    PO4  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
    AC4  [ RasMol ]  +environment [ RasMol ]
    AC5  [ RasMol ]  +environment [ RasMol ]
    AC6  [ RasMol ]  +environment [ RasMol ]
    AC7  [ RasMol ]  +environment [ RasMol ]
    AC8  [ RasMol ]  +environment [ RasMol ]
    AC9  [ RasMol ]  +environment [ RasMol ]
    BC1  [ RasMol ]  +environment [ RasMol ]
    BC2  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 4le2)
 
Biological Units
  Complete Structure
    Biological Unit 1  [ Jena3D ]
    Biological Unit 2  [ Jena3D ]
    Biological Unit 3  [ Jena3D ]
    Biological Unit 4  [ 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 | Biol. Unit 3 PNG format | Biol. Unit 4 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
  4le2
    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
  DESR_BACSU | O34723
    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
  DESR_BACSU | O34723
    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
        DESR_BACSU | O34723: 4ldz 4le0 4le1 5iuj 5iuk 5iul 5iun

(-) Related Entries Specified in the PDB File

4ldz 4le0 4le1