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 HALOQUADRATUM WALSBYI BACTERIORHODOPSIN
 
Authors :  A. H. J. Wang, M. F. Hsu, C. S. Yang, H. Y. Fu
Date :  30 May 14  (Deposition) - 29 Jul 15  (Release) - 29 Jul 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.57
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Bacteriorhodopsin, Proton Pump, Membrane, Membrane Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. H. J. Wang, M. F. Hsu, C. S. Yang, H. Y. Fu, C. J. Cai, H. P. Yi
An Acid-Tolerant Light-Driven Proton Pump
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - BACTERIORHODOPSIN-I
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET21D
    Expression System Strain: C43 (DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: BOP1, BOPI, HQ_1014A
    Organism Scientific: HALOQUADRATUM WALSBYI
    Organism Taxid: 362976
    Strain: DSM 16790 / HBSQ001

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 5)

Asymmetric/Biological Unit (3, 5)
No.NameCountTypeFull Name
1ACT2Ligand/IonACETATE ION
2MPG1Ligand/Ion1-MONOOLEOYL-RAC-GLYCEROL
3RET2Ligand/IonRETINAL

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETYR A:91 , TRP A:94 , THR A:98 , MET A:126 , GLY A:130 , TRP A:146 , SER A:149 , THR A:150 , MET A:153 , TRP A:190 , TYR A:193 , PRO A:194 , ALA A:223 , LYS A:224BINDING SITE FOR RESIDUE RET A 301
2AC2SOFTWAREGLU A:75 , SER A:77BINDING SITE FOR RESIDUE ACT A 302
3AC3SOFTWAREARG A:183 , HOH A:435 , ALA B:79 , ASN B:80 , VAL B:139BINDING SITE FOR RESIDUE ACT A 303
4AC4SOFTWARETRP B:94 , THR B:97 , THR B:98 , GLY B:130 , TRP B:146 , SER B:149 , THR B:150 , TRP B:190 , TYR B:193 , PRO B:194 , TRP B:197 , LYS B:224BINDING SITE FOR RESIDUE RET B 301
5AC5SOFTWAREARG B:114 , GLY B:121 , GLU B:173 , ARG B:176 , SER B:177 , ASN B:180 , ALA B:181 , ASN B:184 , HOH B:437BINDING SITE FOR RESIDUE MPG B 302

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4QID)

(-) 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:228
                                                                                                                                                                                                                                                                    
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ....hhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhh...eeee.....eeee.hhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4qid A  12 GVEGEGIWLALGTIGMLLGMLYFIADGLDVQDPRQKEFYVITILIPAIAAASYLSMFFGFGLTEVSLANGRVVDVYWARYADWLFTTPLLLLDIGLLAGASQRDIGALVGIDAFMIVTGLVATLTKVVVARYAFWTISTISMVFLLYYLVAVFGEAVSDADEDTRSTFNALRNIILVTWAIYPVAWLVGTEGLALTGLYGETLLFMVLDLVAKVGFGFILLRSRAIMG 239
                                    21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231        


Chain B from PDB  Type:PROTEIN  Length:224
                                                                                                                                                                                                                                                                
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhh....eee.....eee..hhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4qid B  14 EGEGIWLALGTIGMLLGMLYFIADGLDVQDPRQKEFYVITILIPAIAAASYLSMFFGFGLTEVSLANGRVVDVYWARYADWLFTTPLLLLDIGLLAGASQRDIGALVGIDAFMIVTGLVATLTKVVVARYAFWTISTISMVFLLYYLVAVFGEAVSDADEDTRSTFNALRNIILVTWAIYPVAWLVGTEGLALTGLYGETLLFMVLDLVAKVGFGFILLRSRAI 237
                                    23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233
   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 4QID)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (12, 12)

Asymmetric/Biological Unit(hide GO term definitions)

 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
    ACT  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    MPG  [ 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 ]
    AC5  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 4qid)
 

(-) 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
  4qid
    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
  BACR1_HALWD | Q18DH8
    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
  BACR1_HALWD | Q18DH8
    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
        BACR1_HALWD | Q18DH8: 4qi1 5itc 5ite 5kkh

(-) Related Entries Specified in the PDB File

4qi1 THE SAME PROTEIN WITH TRIMERIC PACKING.