Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asym.Unit - manually
(-)Asymmetric Unit
(-)Biological Unit 1
(-)Biological Unit 2
collapse expand < >
Image Asym.Unit - manually
Asym.Unit - manually  (Jmol Viewer)
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 :  ANABAENA SENSORY RHODOPSIN TRANSDUCER
 
Authors :  L. Vogeley
Date :  27 Sep 06  (Deposition) - 20 Mar 07  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.80
Chains :  Asym. Unit :  A,B,C,D,E,F,G,H
Biol. Unit 1:  A,B,F,H  (1x)
Biol. Unit 2:  C,D,E,G  (1x)
Keywords :  Rhodopsin, Transducer, Signaling Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  L. Vogeley, V. D. Trivedi, O. A. Sineshchekov, E. N. Spudich, J. L. Spudich, H. Luecke
Crystal Structure Of The Anabaena Sensory Rhodopsin Transducer.
J. Mol. Biol. V. 367 741 2007
PubMed-ID: 17289074  |  Reference-DOI: 10.1016/J.JMB.2006.11.074
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - ANABAENA SENSORY RHODOPSIN TRANSDUCER PROTEIN
    Chains: A, B, C, D, E, F, G, H
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21
    Expression System Plasmid: PKJ
    Expression System Strain: BL21
    Expression System Taxid: 511693
    Expression System Vector Type: PLASMID
    Organism Scientific: ANABAENA SP.
    Organism Taxid: 1167

 Structural Features

(-) Chains, Units

  12345678
Asymmetric Unit : ABCDEFGH
Biological Unit 1 (1x): AB   F H
Biological Unit 2 (1x):   CDE G 

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 2II7)

(-) Sites  (0, 0)

(no "Site" information available for 2II7)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2II7)

(-) Cis Peptide Bonds  (8, 8)

Asymmetric Unit
No.Residues
1Asp A:79 -Pro A:80
2Asp B:79 -Pro B:80
3Asp C:79 -Pro C:80
4Asp D:79 -Pro D:80
5Asp E:79 -Pro E:80
6Asp F:79 -Pro F:80
7Asp G:79 -Pro G:80
8Asp H:79 -Pro H:80

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2II7)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2II7)

(-) Exons   (0, 0)

(no "Exon" information available for 2II7)

(-) 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:112
 aligned with Q8YSC3_NOSS1 | Q8YSC3 from UniProtKB/TrEMBL  Length:125

    Alignment length:119
                                    11        21        31        41        51        61        71        81        91       101       111         
         Q8YSC3_NOSS1     2 SLSIGRTCWAIAEGYIPPYGNGPEPQFISHETVCILNAGDEDAHVEITIYYSDKEPVGPYRLTVPARRTKHVRFNDLNDPAPIPHDTDFASVIQSNVPIVVQHTRLDSRQAENALLSTI 120
               SCOP domains d2ii7a_ A: automa       ted matches                                                                                     SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeeee......-------.......eeeeee.....eeeeeeeee.....eeeeeeee...eeeeee.hhh...........eeeeeeeeeeeeee..hhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------- Transcript
                 2ii7 A   1 SLSIGRTCWAIAEGYIP-------PQFISHETVCILNAGDEDAHVEITIYYSDKEPVGPYRLTVPARRTKHVRFNDLNDPAPIPHDTDFASVIQSNVPIVVQHTRLDSRQAENALLSTI 119
                                    10      |  -    |   30        40        50        60        70        80        90       100       110         
                                           17      25                                                                                              


Chain B from PDB  Type:PROTEIN  Length:115
 aligned with Q8YSC3_NOSS1 | Q8YSC3 from UniProtKB/TrEMBL  Length:125

    Alignment length:115
                                    12        22        32        42        52        62        72        82        92       102       112     
         Q8YSC3_NOSS1     3 LSIGRTCWAIAEGYIPPYGNGPEPQFISHETVCILNAGDEDAHVEITIYYSDKEPVGPYRLTVPARRTKHVRFNDLNDPAPIPHDTDFASVIQSNVPIVVQHTRLDSRQAENALL 117
               SCOP domains d2ii7b_ B: automated matches                                                                                        SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeee....................eeeeee.....eeeeeeeee.....eeeeeeee...eeeeee.hhh...........eeeeeeeeeeeeeeee..hhhhhh.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------- Transcript
                 2ii7 B   2 LSIGRTCWAIAEGYIPPYGNGPEPQFISHETVCILNAGDEDAHVEITIYYSDKEPVGPYRLTVPARRTKHVRFNDLNDPAPIPHDTDFASVIQSNVPIVVQHTRLDSRQAENALL 116
                                    11        21        31        41        51        61        71        81        91       101       111     


Chain C from PDB  Type:PROTEIN  Length:110
 aligned with Q8YSC3_NOSS1 | Q8YSC3 from UniProtKB/TrEMBL  Length:125

    Alignment length:120
                                    11        21        31        41        51        61        71        81        91       101       111       121
         Q8YSC3_NOSS1     2 SLSIGRTCWAIAEGYIPPYGNGPEPQFISHETVCILNAGDEDAHVEITIYYSDKEPVGPYRLTVPARRTKHVRFNDLNDPAPIPHDTDFASVIQSNVPIVVQHTRLDSRQAENALLSTIA 121
               SCOP domains d2ii7c_ C: automat          ed matches                                                                                   SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .....eeeeee.......----------...eeeeee.....eeeeeeeee.....eeeeeeee...eeeeee.hhh...........eeeeeeeeeeeeee..hhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------ Transcript
                 2ii7 C   1 SLSIGRTCWAIAEGYIPP----------SHETVCILNAGDEDAHVEITIYYSDKEPVGPYRLTVPARRTKHVRFNDLNDPAPIPHDTDFASVIQSNVPIVVQHTRLDSRQAENALLSTIA 120
                                    10       | -        30        40        50        60        70        80        90       100       110       120
                                            18         29                                                                                           


Chain D from PDB  Type:PROTEIN  Length:103
 aligned with Q8YSC3_NOSS1 | Q8YSC3 from UniProtKB/TrEMBL  Length:125

    Alignment length:106
                                    11        21        31        41        51        61        71        81        91       101      
         Q8YSC3_NOSS1     2 SLSIGRTCWAIAEGYIPPYGNGPEPQFISHETVCILNAGDEDAHVEITIYYSDKEPVGPYRLTVPARRTKHVRFNDLNDPAPIPHDTDFASVIQSNVPIVVQHTRL 107
               SCOP domains d2ii7d_ D: automated match   es                                                                            SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeeee...............---..eeeeee.....eeeeeeee......eeeeeeee...eeeeee.hhh............eeeeeeeeeeeeee... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------- Transcript
                 2ii7 D   1 SLSIGRTCWAIAEGYIPPYGNGPEPQ---HETVCILNAGDEDAHVEITIYYSDKEPVGPYRLTVPARRTKHVRFNDLNDPAPIPHDTDFASVIQSNVPIVVQHTRL 106
                                    10        20     |  30        40        50        60        70        80        90       100      
                                                    26  30                                                                            


Chain E from PDB  Type:PROTEIN  Length:106
 aligned with Q8YSC3_NOSS1 | Q8YSC3 from UniProtKB/TrEMBL  Length:125

    Alignment length:113
                                    11        21        31        41        51        61        71        81        91       101       111   
         Q8YSC3_NOSS1     2 SLSIGRTCWAIAEGYIPPYGNGPEPQFISHETVCILNAGDEDAHVEITIYYSDKEPVGPYRLTVPARRTKHVRFNDLNDPAPIPHDTDFASVIQSNVPIVVQHTRLDSRQAEN 114
               SCOP domains d2ii7e_ E: automated ma       tches                                                                               SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeeee............-------.eeeeee.....eeeeeeeee.....eeeeeeee...eeeeee.hhh...........eeeeeeeeeeeeeeee..hhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------- Transcript
                 2ii7 E   1 SLSIGRTCWAIAEGYIPPYGNGP-------ETVCILNAGDEDAHVEITIYYSDKEPVGPYRLTVPARRTKHVRFNDLNDPAPIPHDTDFASVIQSNVPIVVQHTRLDSRQAEN 113
                                    10        20  |      -|       40        50        60        70        80        90       100       110   
                                                 23      31                                                                                  


Chain F from PDB  Type:PROTEIN  Length:91
 aligned with Q8YSC3_NOSS1 | Q8YSC3 from UniProtKB/TrEMBL  Length:125

    Alignment length:103
                                    12        22        32        42        52        62        72        82        92       102   
         Q8YSC3_NOSS1     3 LSIGRTCWAIAEGYIPPYGNGPEPQFISHETVCILNAGDEDAHVEITIYYSDKEPVGPYRLTVPARRTKHVRFNDLNDPAPIPHDTDFASVIQSNVPIVVQHT 105
               SCOP domains d2ii7f_ F: automa            ted matches                                                                SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeee.......------------.eeeeee.....eeeeeeeee.....eeeeeeee...eeeeee.hhh...........eeeeeeeeeeeeeeee Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------- Transcript
                 2ii7 F   2 LSIGRTCWAIAEGYIPP------------ETVCILNAGDEDAHVEITIYYSDKEPVGPYRLTVPARRTKHVRFNDLNDPAPIPHDTDFASVIQSNVPIVVQHT 104
                                    11      |  -        31        41        51        61        71        81        91       101   
                                           18           31                                                                         


Chain G from PDB  Type:PROTEIN  Length:91
 aligned with Q8YSC3_NOSS1 | Q8YSC3 from UniProtKB/TrEMBL  Length:125

    Alignment length:103
                                    12        22        32        42        52        62        72        82        92       102   
         Q8YSC3_NOSS1     3 LSIGRTCWAIAEGYIPPYGNGPEPQFISHETVCILNAGDEDAHVEITIYYSDKEPVGPYRLTVPARRTKHVRFNDLNDPAPIPHDTDFASVIQSNVPIVVQHT 105
               SCOP domains d2ii7g_ G: automa            ted matches                                                                SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeee.......------------.eeeeee.....eeeeeeeee.....eeeeeeee...eeeeee.hhh...........eeeeeeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------- Transcript
                 2ii7 G   2 LSIGRTCWAIAEGYIPP------------ETVCILNAGDEDAHVEITIYYSDKEPVGPYRLTVPARRTKHVRFNDLNDPAPIPHDTDFASVIQSNVPIVVQHT 104
                                    11      |  -        31        41        51        61        71        81        91       101   
                                           18           31                                                                         


Chain H from PDB  Type:PROTEIN  Length:106
 aligned with Q8YSC3_NOSS1 | Q8YSC3 from UniProtKB/TrEMBL  Length:125

    Alignment length:118
                                    11        21        31        41        51        61        71        81        91       101       111        
         Q8YSC3_NOSS1     2 SLSIGRTCWAIAEGYIPPYGNGPEPQFISHETVCILNAGDEDAHVEITIYYSDKEPVGPYRLTVPARRTKHVRFNDLNDPAPIPHDTDFASVIQSNVPIVVQHTRLDSRQAENALLST 119
               SCOP domains d2ii7h_ H: automat            ed matches                                                                               SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeeee.......------------.eeeeee.....eeeeeeeee.....eeeeeeee...eeeeee.hhh...........eeeeeeeeeeeeeee...hhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------- Transcript
                 2ii7 H   1 SLSIGRTCWAIAEGYIPP------------ETVCILNAGDEDAHVEITIYYSDKEPVGPYRLTVPARRTKHVRFNDLNDPAPIPHDTDFASVIQSNVPIVVQHTRLDSRQAENALLST 118
                                    10       | -         -|       40        50        60        70        80        90       100       110        
                                            18           31
   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, 8)

Asymmetric Unit
(-)
Class: All beta proteins (24004)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2II7)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2II7)

(-) Gene Ontology  (0, 0)

Asymmetric Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 2II7)

 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 2ii7)
 
  Sites
(no "Sites" information available for 2ii7)
 
  Cis Peptide Bonds
    Asp A:79 - Pro A:80   [ RasMol ]  
    Asp B:79 - Pro B:80   [ RasMol ]  
    Asp C:79 - Pro C:80   [ RasMol ]  
    Asp D:79 - Pro D:80   [ RasMol ]  
    Asp E:79 - Pro E:80   [ RasMol ]  
    Asp F:79 - Pro F:80   [ RasMol ]  
    Asp G:79 - Pro G:80   [ RasMol ]  
    Asp H:79 - Pro H:80   [ 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 | 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
  2ii7
    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
  Q8YSC3_NOSS1 | Q8YSC3
    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
  Q8YSC3_NOSS1 | Q8YSC3
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/TrEMBL
        Q8YSC3_NOSS1 | Q8YSC3: 2ii8 2ii9 2iia

(-) Related Entries Specified in the PDB File

2ii8 2ii9 2iia