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
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)

(-) Description

Title :  CRYSTAL STRUCTURE OF BLUE LIGHT-ABSORBING PROTEORHODOPSIN FROM MED12 AT 2.3 ANGSTROM
 
Authors :  G. Ozorowski, H. Luecke
Date :  20 Mar 13  (Deposition) - 08 May 13  (Release) - 23 Oct 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.31
Chains :  Asym. Unit :  A,B,C
Biol. Unit 1:  A,B,C  (2x)
Keywords :  Retinylidene Protein, Ion Transport, Proton Transport (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  T. Ran, G. Ozorowski, Y. Gao, O. A. Sineshchekov, W. Wang, J. L. Spudich H. Luecke
Cross-Protomer Interaction With The Photoactive Site In Oligomeric Proteorhodopsin Complexes.
Acta Crystallogr. , Sect. D V. 69 1965 2013
PubMed-ID: 24100316  |  Reference-DOI: 10.1107/S0907444913017575

(-) Compounds

Molecule 1 - PROTEORHODOPSIN
    Chains: A, B, C
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: C43(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PET28A
    Gene: PROTEORHODOPSIN
    Organism Scientific: UNCULTURED BACTERIUM
    Organism Taxid: 77133

 Structural Features

(-) Chains, Units

  123
Asymmetric Unit : ABC
Biological Unit 1 (2x): ABC

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 5)

Asymmetric Unit (2, 5)
No.NameCountTypeFull Name
1LI12Ligand/Ion1-[2,6,10.14-TETRAMETHYL-HEXADECAN-16-YL]-2-[2,10,14-TRIMETHYLHEXADECAN-16-YL]GLYCEROL
2RET3Ligand/IonRETINAL
Biological Unit 1 (2, 10)
No.NameCountTypeFull Name
1LI14Ligand/Ion1-[2,6,10.14-TETRAMETHYL-HEXADECAN-16-YL]-2-[2,10,14-TRIMETHYLHEXADECAN-16-YL]GLYCEROL
2RET6Ligand/IonRETINAL

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETRP A:80 , THR A:83 , VAL A:84 , GLN A:87 , MET A:116 , GLY A:120 , TRP A:134 , GLY A:137 , TRP A:180 , TYR A:183 , TYR A:187 , ASP A:209 , LYS A:213BINDING SITE FOR RESIDUE RET A 301
2AC2SOFTWARETYR B:77 , TRP B:80 , THR B:83 , VAL B:84 , GLN B:87 , MET B:116 , GLY B:120 , TRP B:134 , GLY B:137 , TRP B:141 , TRP B:180 , TYR B:183 , ASP B:209 , LYS B:213BINDING SITE FOR RESIDUE RET B 301
3AC3SOFTWAREPHE B:30 , ARG B:33BINDING SITE FOR RESIDUE LI1 B 302
4AC4SOFTWARETRP C:80 , THR C:83 , VAL C:84 , GLN C:87 , MET C:116 , GLY C:120 , TRP C:141 , TRP C:180 , TYR C:183 , ASP C:209 , LYS C:213BINDING SITE FOR RESIDUE RET C 301

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4JQ6)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Phe A:169 -Asn A:170

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4JQ6)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4JQ6)

(-) Exons   (0, 0)

(no "Exon" information available for 4JQ6)

(-) 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:197
                                                                                                                                                                                                                                     
               SCOP domains d4jq6a_ A: automated matches                                                                                                                                                                          SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4jq6 A   9 DYVGISFWLAAAIMLASTVFFFVERSDVPVKWKTSLTVAGLVTGVAFWHYLYMRGVWIYAGETPTVFRYIDWLITVPLQIIEFYLIIAVFWKLLIASLVMLIGGFIGEAGLGDVVVWWIVGMIAWLYIIYEIFLFNTIKWIVTVGWAIYPIGYAWGYFGDGLNEDALNIVYNLADLINKAAFGLAIWAAAMKDKETS 231
                                    18        28        38        48        58        68        78        88       106       116       126       136       146   ||  174       184       194       204       214       224       
                                                                                                                  96|                                          150|                                                              
                                                                                                                  105                                           169                                                              


Chain B from PDB  Type:PROTEIN  Length:203
                                                                                                                                                                                                                                           
               SCOP domains d4jq6b_ B: automated matches                                                                                                                                                                                SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4jq6 B   9 DYVGISFWLAAAIMLASTVFFFVERSDVPVKWKTSLTVAGLVTGVAFWHYLYMRGVWIYAGETPTVFRYIDWLITVPLQIIEFYLIIAAAVFWKLLIASLVMLIGGFIGEAGLGDVVVWWIVGMIAWLYIIYEIFLGAASQQAFNTIKWIVTVGWAIYPIGYAWGYFGDGLNEDALNIVYNLADLINKAAFGLAIWAAAMKDK 228
                                    18        28        38        48        58        68        78        88       104       114       124       134       144      |165       175       185       195       205       215       225   
                                                                                                                   97|                                            151|                                                                 
                                                                                                                   104                                             163                                                                 


Chain C from PDB  Type:PROTEIN  Length:199
                                                                                                                                                                                                                                       
               SCOP domains d4jq6c_ C: automated matches                                                                                                                                                                            SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4jq6 C   9 DYVGISFWLAAAIMLASTVFFFVERSDVPVKWKTSLTVAGLVTGVAFWHYLYMRGVWIYAGETPTVFRYIDWLITVPLQIIEFYLIIAVFWKLLIASLVMLIGGFIGEAGLGDVVVWWIVGMIAWLYIIYEIFSQQAFNTIKWIVTVGWAIYPIGYAWGYFGDGLNEDALNIVYNLADLINKAAFGLAIWAAAMKDKET 230
                                    18        28        38        48        58        68        78        88       106       116       126       136       146  ||   171       181       191       201       211       221         
                                                                                                                  96|                                         149|                                                                 
                                                                                                                  105                                          165
   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, 3)

Asymmetric Unit
(-)
Class: Membrane and cell surface proteins and peptides (2046)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4JQ6)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4JQ6)

(-) Gene Ontology  (8, 8)

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
    LI1  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    RET  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
    AC4  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Phe A:169 - Asn A:170   [ RasMol ]  
 
Biological Unit
  Complete Structure
    Biological Unit 1  [ 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 ](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
  4jq6
    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
  Q4PP54_9BACT | Q4PP54
    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
  Q4PP54_9BACT | Q4PP54
    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 4JQ6)

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 4JQ6)