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 :  STRUCTURES OF ICT AND PR1 INTERMEDIATES FROM TIME-RESOLVED LAUE CRYSTALLOGRAPHY COLLECTED AT 14ID-B, APS
 
Authors :  Y. O. Jung, J. H. Lee, J. Kim, M. Schmidt, S. Vukica, K. Moffat, H. Ihee
Date :  26 Nov 12  (Deposition) - 20 Mar 13  (Release) - 20 Mar 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.60
Chains :  Asym./Biol. Unit :  A
Keywords :  Photoreceptor, Chromophore, Photoreceptor Protein, Receptor, Sensory Transduction, Luminescent Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  Y. O. Jung, J. H. Lee, J. Kim, M. Schmidt, K. Moffat, V. Srajer, H. Ihee
Volume-Conserving Trans-Cis Isomerization Pathways In Photoactive Yellow Protein Visualized By Picosecond X-Ray Crystallography
Nat. Chem. V. 5 212 2013
PubMed-ID: 23422563  |  Reference-DOI: 10.1038/NCHEM.1565

(-) Compounds

Molecule 1 - PHOTOACTIVE YELLOW PROTEIN
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPQE80
    Expression System StrainM15
    Expression System Taxid562
    Expression System Vector TypePLASMID
    GenePYP
    Organism ScientificHALORHODOSPIRA HALOPHILA
    Organism Taxid1053
    SynonymPYP

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 1)

Asymmetric/Biological Unit (1, 1)
No.NameCountTypeFull Name
1HC41Ligand/Ion4'-HYDROXYCINNAMIC ACID

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETYR A:42 , GLU A:46 , THR A:50 , ARG A:52 , PHE A:62 , VAL A:66 , ALA A:67 , CYS A:69 , THR A:70 , PHE A:96 , TYR A:98BINDING SITE FOR RESIDUE HC4 A 201

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4I39)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4I39)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4I39)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4I39)

(-) Exons   (0, 0)

(no "Exon" information available for 4I39)

(-) 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:125
                                                                                                                                                             
               SCOP domains d4i39a_ A: Photoactive yellow protein, PYP                                                                                    SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........hhhhhhh..hhhhhh......eee.....eeeehhhhhhhhh...............hhhhh...hhhhhhhhhhhh..eeeeeeee......eeeeeeeee......eeeeeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------- Transcript
                 4i39 A   1 MEHVAFGSEDIENTLAKMDDGQLDGLAFGAIQLDGDGNILQYNAAEGDITGRDPKQVIGKNFFKDVAPCTDSPEFYGKFKEGVASGNLNTMFEYTFDYQMTPTKVKVHMKKALSGDSYWVFVKRV 125
                                    10        20        30        40        50        60        70        80        90       100       110       120     

   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, 1)

Asymmetric/Biological Unit

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4I39)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4I39)

(-) Gene Ontology  (5, 5)

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
    HC4  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 4i39)
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  4i39
    Family and Domain InformationProDom | SYSTERS
    General Structural InformationGlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in MembranesOPM
    Protein SurfaceSURFACE
    Secondary StructureDSSP (structure derived) | HSSP (homology derived)
    Structural GenomicsGeneCensus
    Structural NeighboursCE | VAST
    Structure ClassificationCATH | Dali | SCOP
    Validation and Original DataBMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  PYP_HALHA | P16113
    Comparative Protein Structure ModelsModBase
    Genomic InformationEnsembl
    Protein-protein InteractionDIP
    Sequence, Family and Domain InformationInterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  (no 'Enzyme Classificator' available)
    General Enzyme InformationBRENDA | EC-PDB | Enzyme | IntEnz
    PathwayKEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease InformationOMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related InformationGenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain InformationXDom
    Interatomic Contacts of Structural UnitsCSU
    Ligand-protein ContactsLPC
    Protein CavitiescastP
    Sequence and Secondary StructurePDBCartoon
    Structure AlignmentSTRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence BrowserSTING
 
Access by UniProt ID/Accession number
  PYP_HALHA | P16113
    Protein Disorder PredictionDisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        PYP_HALHA | P161131d7e 1f98 1f9i 1gsv 1gsw 1gsx 1kou 1nwz 1odv 1ot6 1ot9 1ota 1otb 1otd 1ote 1oti 1s1y 1s1z 1s4r 1s4s 1t18 1t19 1t1a 1t1b 1t1c 1ts0 1ts6 1ts7 1ts8 1ugu 1uwn 1uwp 1xfn 1xfq 2d01 2d02 2i9v 2kx6 2phy 2pyp 2pyr 2qj5 2qj7 2qws 2zoh 2zoi 3phy 3pyp 3umd 3ume 3ve3 3ve4 4b9o 4bbt 4bbu 4bbv 4hy8 4i38 4i3a 4i3i 4i3j 4wl9 4wla 5hd3 5hd5 5hdc 5hdd 5hds

(-) Related Entries Specified in the PDB File

1ts0 1ts6 1ts7 1ts8 3ve3 3ve4 4hy8 4i38 4i3a 4i3i 4i3j