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
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)

(-) Description

Title :  CRYSTAL STRUCTURE OF A MONOMERIC CYAN FLUORESCENT PROTEIN IN THE PHOTOBLEACHED STATE
 
Authors :  J. N. Henderson, H. Ai, R. E. Campbell, S. J. Remington
Date :  07 Feb 07  (Deposition) - 03 Apr 07  (Release) - 22 Feb 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.47
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Beta Can, Fluorescent Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. N. Henderson, H. W. Ai, R. E. Campbell, S. J. Remington
Structural Basis For Reversible Photobleaching Of A Green Fluorescent Protein Homologue.
Proc. Natl. Acad. Sci. Usa V. 104 6672 2007
PubMed-ID: 17420458  |  Reference-DOI: 10.1073/PNAS.0700059104

(-) Compounds

Molecule 1 - GFP-LIKE FLUORESCENT CHROMOPROTEIN CFP484
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PBAD/HISB
    Expression System Strain: TOP10
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: CFP484
    Mutation: YES
    Organism Scientific: CLAVULARIA SP.
    Organism Taxid: 86521

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): A 
Biological Unit 2 (1x):  B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 3)

Asymmetric Unit (2, 3)
No.NameCountTypeFull Name
1ACT1Ligand/IonACETATE ION
2PIA2Mod. Amino Acid[(4Z)-2-[(1S)-1-AMINOETHYL]-4-(4-HYDROXYBENZYLIDENE)-5-OXO-4,5-DIHYDRO-1H-IMIDAZOL-1-YL]ACETIC ACID
Biological Unit 1 (2, 2)
No.NameCountTypeFull Name
1ACT1Ligand/IonACETATE ION
2PIA1Mod. Amino Acid[(4Z)-2-[(1S)-1-AMINOETHYL]-4-(4-HYDROXYBENZYLIDENE)-5-OXO-4,5-DIHYDRO-1H-IMIDAZOL-1-YL]ACETIC ACID
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1ACT-1Ligand/IonACETATE ION
2PIA1Mod. Amino Acid[(4Z)-2-[(1S)-1-AMINOETHYL]-4-(4-HYDROXYBENZYLIDENE)-5-OXO-4,5-DIHYDRO-1H-IMIDAZOL-1-YL]ACETIC ACID

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY A:33 , GLU A:34 , THR A:43 , ASP B:160BINDING SITE FOR RESIDUE ACT A 1

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (4, 4)

Asymmetric Unit
No.Residues
1Ala A:52 -Pro A:53
2Phe A:87 -Pro A:88
3Ala B:52 -Pro B:53
4Phe B:87 -Pro B:88

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 2OTE)

(-) 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:214
 aligned with GFPL_CLASP | Q9U6Y3 from UniProtKB/Swiss-Prot  Length:266

    Alignment length:216
                                    53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253      
           GFPL_CLASP    44 GVIKPDMKIKLKMEGNVNGHAFVIEGEGEGKPYDGTHTLNLEVKEGAPLPFSYDILSNAFQYGNRALTKYPDDIADYFKQSFPEGYSWERTMTFEDKGIVKVKSDISMEEDSFIYEIRFDGMNFPPNGPVMQKKTLKWEPSTEIMYVRDGVLVGDISHSLLLEGGGHYRCDFKSIYKAKKVVKLPDYHFVDHRIEILNHDKDYNKVTLYENAVARY 259
               SCOP domains d2otea_ A: automated matches                                                                                                                                                                                             SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ......eeeeeeeeeee..eeeeeeeeeeee....eeeeeeeeee.......hhhhhh...--............hhhhhh....eeeeeeeee....eeeeeeeeeee..eeeeeeeeeee............eeee..eeeeeeee..eeeeeeeeeeee....eeeeeeeeeeee.........eeeeeeeeeeee.....eeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2ote A   6 GVIKPDMKIKLKMEGNVNGHAFVIEGEGEGKPYDGTNTINLEVKEGAPLPFSYDILTNAFa--NRAFTKYPDDIPNYFKQSFPEGYSWERTMTFEDKGIVKVKSDISMEEDSFIYEIHLKGENFPPNGPVMQKKTLKWEPSTEILYVRDGVLVGDIKHKLLLEGGGHHRVDFKTIYRAKKAVKLPDYHFVDHRIEILNHDKDYNKVTVYESAVARY 221
                                    15        25        35        45        55        65|  |    75        85        95       105       115       125       135       145       155       165       175       185       195       205       215      
                                                                                       66-PIA                                                                                                                                                       


Chain B from PDB  Type:PROTEIN  Length:214
 aligned with GFPL_CLASP | Q9U6Y3 from UniProtKB/Swiss-Prot  Length:266

    Alignment length:216
                                    53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253      
           GFPL_CLASP    44 GVIKPDMKIKLKMEGNVNGHAFVIEGEGEGKPYDGTHTLNLEVKEGAPLPFSYDILSNAFQYGNRALTKYPDDIADYFKQSFPEGYSWERTMTFEDKGIVKVKSDISMEEDSFIYEIRFDGMNFPPNGPVMQKKTLKWEPSTEIMYVRDGVLVGDISHSLLLEGGGHYRCDFKSIYKAKKVVKLPDYHFVDHRIEILNHDKDYNKVTLYENAVARY 259
               SCOP domains d2oteb_ B: automated matches                                                                                                                                                                                             SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
           Pfam domains (1) GFP-2oteB01 B:6-221                                                                                                                                                                                                      Pfam domains (1)
           Pfam domains (2) GFP-2oteB02 B:6-221                                                                                                                                                                                                      Pfam domains (2)
         Sec.struct. author ......eeeeeeeeeee..eeeeeeeeeeee....eeeeeeeeee.......hhhhhh...--............hhhhhh....eeeeeeeee....eeeeeeeeeee..eeeeeeeeeee............eeee..eeeeeeee..eeeeeeeeeeee....eeeeeeeeeeee.........eeeeeeeeeeee.....eeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2ote B   6 GVIKPDMKIKLKMEGNVNGHAFVIEGEGEGKPYDGTNTINLEVKEGAPLPFSYDILTNAFa--NRAFTKYPDDIPNYFKQSFPEGYSWERTMTFEDKGIVKVKSDISMEEDSFIYEIHLKGENFPPNGPVMQKKTLKWEPSTEILYVRDGVLVGDIKHKLLLEGGGHHRVDFKTIYRAKKAVKLPDYHFVDHRIEILNHDKDYNKVTVYESAVARY 221
                                    15        25        35        45        55        65|  |    75        85        95       105       115       125       135       145       155       165       175       185       195       205       215      
                                                                                       66-PIA
   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, 2)

Asymmetric Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (1, 2)

Asymmetric Unit
(-)
Clan: GFP (101)

(-) Gene Ontology  (3, 3)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (GFPL_CLASP | Q9U6Y3)
biological process
    GO:0008218    bioluminescence    The production of light by certain enzyme-catalyzed reactions in cells.
    GO:0006091    generation of precursor metabolites and energy    The chemical reactions and pathways resulting in the formation of precursor metabolites, substances from which energy is derived, and any process involved in the liberation of energy from these substances.
    GO:0018298    protein-chromophore linkage    The covalent or noncovalent attachment of a chromophore to a protein.

 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
    ACT  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    PIA  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Ala A:52 - Pro A:53   [ RasMol ]  
    Ala B:52 - Pro B:53   [ RasMol ]  
    Phe A:87 - Pro A:88   [ RasMol ]  
    Phe B:87 - Pro B:88   [ 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 | Asym. Unit - sites PNG format | Biol. Unit 1 PNG format | Biol. Unit 1 - sites 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
  2ote
    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
  GFPL_CLASP | Q9U6Y3
    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
  GFPL_CLASP | Q9U6Y3
    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
        GFPL_CLASP | Q9U6Y3: 2hqk 2otb 4q9w 4q9x 4r6d

(-) Related Entries Specified in the PDB File

2otb CRYSTAL STRUCTURE OF A MONOMERIC CYAN FLUORESCENT PROTEIN IN THE FLUORESCENT STATE