Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asym./Biol. Unit
collapse expand < >
Image Asym./Biol. Unit
Asym./Biol. Unit  (Jmol Viewer)

(-) Description

Title :  CRYSTAL STRUCTURE OF YELLOW FLUORESCENT PROTEIN FROM ZOANTHUS SP. AT 1.8 A RESOLUTION
 
Authors :  N. V. Pletneva, S. V. Pletnev, T. V. Tikhonova, V. Z. Pletnev
Date :  08 Jan 07  (Deposition) - 25 Sep 07  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Gfp-Like Proteins, Yellow Fluorescent Protein, Zoanthus Sp. , Chromophore Structure, Tetramer Structure, Intermonomer Interfaces (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  N. V. Pletneva, S. V. Pletnev, D. M. Chudakov, T. V. Tikhonova, V. O. Popov, V. I. Martynov, A. Wlodawer, Z. Dauter, V. Z. Pletnev
Three-Dimensional Structure Of Yellow Fluorescent Protein Zyfp538 From Zoanthus Sp. At The Resolution 1. 8 Angstrom
Bioorg. Khim. V. 33 421
PubMed-ID: 17886433  |  Reference-DOI: 10.1134/S1068162007040048
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - FLUORESCENT PROTEIN FP538
    Chains: A, B, C, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PQE30-ZFP538
    Expression System Strain: JM109 (DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Organism Scientific: ZOANTHUS SP.
    Organism Taxid: 105402

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 8)

Asymmetric/Biological Unit (2, 8)
No.NameCountTypeFull Name
1CH74Mod. Amino Acid[(4Z)-4-(4-HYDROXYBENZYLIDENE)-5-OXO-2-(3,4,5,6-TETRAHYDROPYRIDIN-2-YL)-4,5-DIHYDRO-1H-IMIDAZOL-1-YL]ACETIC ACID
2NFA4Mod. Amino AcidPHENYLALANINE AMIDE

(-) Sites  (0, 0)

(no "Site" information available for 2OGR)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (8, 8)

Asymmetric/Biological Unit
No.Residues
1Gly A:52 -Pro A:53
2Cys A:87 -Pro A:88
3Gly B:52 -Pro B:53
4Cys B:87 -Pro B:88
5Gly C:52 -Pro C:53
6Cys C:87 -Pro C:88
7Gly D:52 -Pro D:53
8Cys D:87 -Pro D:88

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 2OGR)

(-) 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:224
 aligned with GFPL2_ZOASP | Q9U6Y4 from UniProtKB/Swiss-Prot  Length:231

    Alignment length:226
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225      
          GFPL2_ZOASP     6 HGLKEEMTMKYHMEGCVNGHKFVITGEGIGYPFKGKQTINLCVIEGGPLPFSEDILSAGFKYGDRIFTEYPQDIVDYFKNSCPAGYTWGRSFLFEDGAVCICNVDITVSVKENCIYHKSIFNGMNFPADGPVMKKMTTNWEASCEKIMPVPKQGILKGDVSMYLLLKDGGRYRCQFDTVYKAKSVPSKMPEWHFIQHKLLREDRSDAKNQKWQLTEHAIAFPSALA 231
               SCOP domains d2ogra_ A: automated matches                                                                                                                                                                                                       SCOP domains
               CATH domains 2ogrA00 A:6-231 Green Fluorescent Protein                                                                                                                                                                                          CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eeeeeeeeeee..eeeeeeeeeeeehhh.eeeeeeeeee......hhhhhhhhh.--............hhhhhh....eeeeeeeee....eeeeeeeeeee....eeeeeeeeeee............eeee..eeeeeee......eeeeeeeeeee....eeeeeeeeeeee..........eeeeeeeeeee.......eeeeeeeeeee..... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2ogr A   6 HGLKEEMTMKYHMEGCVNGHKFVITGEGIGYPFKGKQTINLCVIEGGPLPFSEDILSAGfk--DRIFTEYPQDIVDYFKNSCPAGYTWGRSFLFEDGAVCICNVDITVSVKENCIYHKSIFNGMNFPADGPVMKKMTTNWEASCEKIMPVPKQGILKGDVSMYLLLKDGGRYRCQFDTVYKAKSVPSKMPEWHFIQHKLLREDRSDAKNQKWQLTEHAIAFPSALA 231
                                    15        25        35        45        55        65|  |    75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225      
                                                                                      65-NFA                                                                                                                                                                  
                                                                                       66-CH7                                                                                                                                                                 


Chain B from PDB  Type:PROTEIN  Length:224
 aligned with GFPL2_ZOASP | Q9U6Y4 from UniProtKB/Swiss-Prot  Length:231

    Alignment length:226
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225      
          GFPL2_ZOASP     6 HGLKEEMTMKYHMEGCVNGHKFVITGEGIGYPFKGKQTINLCVIEGGPLPFSEDILSAGFKYGDRIFTEYPQDIVDYFKNSCPAGYTWGRSFLFEDGAVCICNVDITVSVKENCIYHKSIFNGMNFPADGPVMKKMTTNWEASCEKIMPVPKQGILKGDVSMYLLLKDGGRYRCQFDTVYKAKSVPSKMPEWHFIQHKLLREDRSDAKNQKWQLTEHAIAFPSALA 231
               SCOP domains d2ogrb_ B: automated matches                                                                                                                                                                                                       SCOP domains
               CATH domains 2ogrB00 B:6-231 Green Fluorescent Protein                                                                                                                                                                                          CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eeeeeeeeeee..eeeeeeeeeeeehhh.eeeeeeeeee......hhhhhhhhh.--............hhhhhh....eeeeeeeee....eeeeeeeeeee....eeeeeeeeeee............eeee..eeeeeee.....eeeeeeeeeeee....eeeeeeeeeeee..........eeeeeeeeeee.......eeeeeeeeeee..... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2ogr B   6 HGLKEEMTMKYHMEGCVNGHKFVITGEGIGYPFKGKQTINLCVIEGGPLPFSEDILSAGfk--DRIFTEYPQDIVDYFKNSCPAGYTWGRSFLFEDGAVCICNVDITVSVKENCIYHKSIFNGMNFPADGPVMKKMTTNWEASCEKIMPVPKQGILKGDVSMYLLLKDGGRYRCQFDTVYKAKSVPSKMPEWHFIQHKLLREDRSDAKNQKWQLTEHAIAFPSALA 231
                                    15        25        35        45        55        65|  |    75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225      
                                                                                      65-NFA                                                                                                                                                                  
                                                                                       66-CH7                                                                                                                                                                 


Chain C from PDB  Type:PROTEIN  Length:224
 aligned with GFPL2_ZOASP | Q9U6Y4 from UniProtKB/Swiss-Prot  Length:231

    Alignment length:226
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225      
          GFPL2_ZOASP     6 HGLKEEMTMKYHMEGCVNGHKFVITGEGIGYPFKGKQTINLCVIEGGPLPFSEDILSAGFKYGDRIFTEYPQDIVDYFKNSCPAGYTWGRSFLFEDGAVCICNVDITVSVKENCIYHKSIFNGMNFPADGPVMKKMTTNWEASCEKIMPVPKQGILKGDVSMYLLLKDGGRYRCQFDTVYKAKSVPSKMPEWHFIQHKLLREDRSDAKNQKWQLTEHAIAFPSALA 231
               SCOP domains d2ogrc_ C: automated matches                                                                                                                                                                                                       SCOP domains
               CATH domains 2ogrC00 C:6-231 Green Fluorescent Protein                                                                                                                                                                                          CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eeeeeeeeeee..eeeeeeeeeeee....eeeeeeeeee......hhhhhhhhh.--............hhhhhh....eeeeeeeee....eeeeeeeeeee....eeeeeeeeeee............eeee..eeeeeee.....eeeeeeeeeeee....eeeeeeeeeeee..........eeeeeeeeeee.......eeeeeeeeeee..... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2ogr C   6 HGLKEEMTMKYHMEGCVNGHKFVITGEGIGYPFKGKQTINLCVIEGGPLPFSEDILSAGfk--DRIFTEYPQDIVDYFKNSCPAGYTWGRSFLFEDGAVCICNVDITVSVKENCIYHKSIFNGMNFPADGPVMKKMTTNWEASCEKIMPVPKQGILKGDVSMYLLLKDGGRYRCQFDTVYKAKSVPSKMPEWHFIQHKLLREDRSDAKNQKWQLTEHAIAFPSALA 231
                                    15        25        35        45        55        65|  |    75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225      
                                                                                      65-NFA                                                                                                                                                                  
                                                                                       66-CH7                                                                                                                                                                 


Chain D from PDB  Type:PROTEIN  Length:224
 aligned with GFPL2_ZOASP | Q9U6Y4 from UniProtKB/Swiss-Prot  Length:231

    Alignment length:226
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225      
          GFPL2_ZOASP     6 HGLKEEMTMKYHMEGCVNGHKFVITGEGIGYPFKGKQTINLCVIEGGPLPFSEDILSAGFKYGDRIFTEYPQDIVDYFKNSCPAGYTWGRSFLFEDGAVCICNVDITVSVKENCIYHKSIFNGMNFPADGPVMKKMTTNWEASCEKIMPVPKQGILKGDVSMYLLLKDGGRYRCQFDTVYKAKSVPSKMPEWHFIQHKLLREDRSDAKNQKWQLTEHAIAFPSALA 231
               SCOP domains d2ogrd_ D: automated matches                                                                                                                                                                                                       SCOP domains
               CATH domains 2ogrD00 D:6-231 Green Fluorescent Protein                                                                                                                                                                                          CATH domains
           Pfam domains (1) GFP-2ogrD01 D:6-228                                                                                                                                                                                                            --- Pfam domains (1)
           Pfam domains (2) GFP-2ogrD02 D:6-228                                                                                                                                                                                                            --- Pfam domains (2)
           Pfam domains (3) GFP-2ogrD03 D:6-228                                                                                                                                                                                                            --- Pfam domains (3)
           Pfam domains (4) GFP-2ogrD04 D:6-228                                                                                                                                                                                                            --- Pfam domains (4)
         Sec.struct. author ......eeeeeeeeeee..eeeeeeeeeeee....eeeeeeeeee......hhhhhhhhh.--............hhhhhh....eeeeeeeee....eeeeeeeeeee....eeeeeeeeeee............eeee..eeeeeee......eeeeeeeeeee....eeeeeeeeeeee..........eeeeeeeeeee.......eeeeeeeeeee..... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2ogr D   6 HGLKEEMTMKYHMEGCVNGHKFVITGEGIGYPFKGKQTINLCVIEGGPLPFSEDILSAGfk--DRIFTEYPQDIVDYFKNSCPAGYTWGRSFLFEDGAVCICNVDITVSVKENCIYHKSIFNGMNFPADGPVMKKMTTNWEASCEKIMPVPKQGILKGDVSMYLLLKDGGRYRCQFDTVYKAKSVPSKMPEWHFIQHKLLREDRSDAKNQKWQLTEHAIAFPSALA 231
                                    15        25        35        45        55        65|  |    75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225      
                                                                                      65-NFA                                                                                                                                                                  
                                                                                       66-CH7
   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, 4)

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

(-) CATH Domains  (1, 4)

Asymmetric/Biological Unit
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (1, 4)

Asymmetric/Biological Unit
(-)
Clan: GFP (101)
(-)
Family: GFP (101)

(-) Gene Ontology  (2, 2)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B,C,D   (GFPL2_ZOASP | Q9U6Y4)
biological process
    GO:0008218    bioluminescence    The production of light by certain enzyme-catalyzed reactions in cells.
    GO:0018298    protein-chromophore linkage    The covalent or noncovalent attachment of a chromophore to a protein.

 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
    CH7  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    NFA  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
(no "Sites" information available for 2ogr)
 
  Cis Peptide Bonds
    Cys A:87 - Pro A:88   [ RasMol ]  
    Cys B:87 - Pro B:88   [ RasMol ]  
    Cys C:87 - Pro C:88   [ RasMol ]  
    Cys D:87 - Pro D:88   [ RasMol ]  
    Gly A:52 - Pro A:53   [ RasMol ]  
    Gly B:52 - Pro B:53   [ RasMol ]  
    Gly C:52 - Pro C:53   [ RasMol ]  
    Gly D:52 - Pro D:53   [ RasMol ]  
 

(-) 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 ](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
  2ogr
    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
  GFPL2_ZOASP | Q9U6Y4
    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
  GFPL2_ZOASP | Q9U6Y4
    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
        GFPL2_ZOASP | Q9U6Y4: 1xa9 1xae

(-) Related Entries Specified in the PDB File

1xa9 1xae