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

(-) Description

Title :  HIGH RESOLUTION CRYSTAL STRUCTURE OF THE DISCOSOMA RED FLUORESCENT PROTEIN (DSRED)
 
Authors :  J. L. Tubbs, J. A. Tainer, E. D. Getzoff
Date :  21 Apr 05  (Deposition) - 02 Aug 05  (Release) - 30 Jun 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.40
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Rfp, Red, Fluorescent Protein, Dsred, Drfp583, Chromophore, Gfp, Coral, Beta Barrel, Beta Can, Luminescent Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. L. Tubbs, J. A. Tainer, E. D. Getzoff
Crystallographic Structures Of Discosoma Red Fluorescent Protein With Immature And Mature Chromophores: Linking Peptide Bond Trans-Cis Isomerization And Acylimine Formation In Chromophore Maturation.
Biochemistry V. 44 9833 2005
PubMed-ID: 16026155  |  Reference-DOI: 10.1021/BI0472907
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - RED FLUORESCENT PROTEIN DRFP583
    Chains: A, B, C, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET15
    Expression System Strain: BL21(DE3) RIL
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Organism Scientific: DISCOSOMA SP.
    Organism Taxid: 86600
    Synonym: DSRED

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 4)

Asymmetric/Biological Unit (1, 4)
No.NameCountTypeFull Name
1CRQ4Mod. Amino Acid[2-(3-CARBAMOYL-1-IMINO-PROPYL)-4-(4-HYDROXY-BENZYLIDENE)-5-OXO-4,5-DIHYDRO-IMIDAZOL-1-YL]-ACETICACID

(-) Sites  (0, 0)

(no "Site" information available for 1ZGO)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1ZGO)

(-) Cis Peptide Bonds  (8, 8)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1ZGO)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1ZGO)

(-) Exons   (0, 0)

(no "Exon" information available for 1ZGO)

(-) 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:218
 aligned with RFP_DISSP | Q9U6Y8 from UniProtKB/Swiss-Prot  Length:225

    Alignment length:220
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225
            RFP_DISSP     6 NVIKEFMRFKVRMEGTVNGHEFEIEGEGEGRPYEGHNTVKLKVTKGGPLPFAWDILSPQFQYGSKVYVKHPADIPDYKKLSFPEGFKWERVMNFEDGGVVTVTQDSSLQDGCFIYKVKFIGVNFPSDGPVMQKKTMGWEASTERLYPRDGVLKGEIHKALKLKDGGHYLVEFKSIYMAKKPVQLPGYYYVDSKLDITSHNEDYTIVEQYERTEGRHHLFL 225
               SCOP domains d1zgoa_ A: automated matches                                                                                                                                                                                                 SCOP domains
               CATH domains 1zgoA00 A:6-225 Green Fluorescent Protein                                                                                                                                                                                    CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eeeeeeeeeee..eeeeeeeeeeee....eeeeeeeeee......hhhhhhhhh.--hhhhh.......hhhhhh....eeeeeeeee....eeeeeeeeeee..eeeeeeeeeee............eeee..eeeeeeee..eeeeeeeeeeee....eeeeeeeeeeee.........eeeeeeeeeeee.....eeeeeeeeeee..... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1zgo A   6 NVIKEFMRFKVRMEGTVNGHEFEIEGEGEGRPYEGHNTVKLKVTKGGPLPFAWDILSPQFq--SKVYVKHPADIPDYKKLSFPEGFKWERVMNFEDGGVVTVTQDSSLQDGCFIYKVKFIGVNFPSDGPVMQKKTMGWEASTERLYPRDGVLKGEIHKALKLKDGGHYLVEFKSIYMAKKPVQLPGYYYVDSKLDITSHNEDYTIVEQYERTEGRHHLFL 225
                                    15        25        35        45        55        65|  |    75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225
                                                                                       66-CRQ                                                                                                                                                           


Chain B from PDB  Type:PROTEIN  Length:218
 aligned with RFP_DISSP | Q9U6Y8 from UniProtKB/Swiss-Prot  Length:225

    Alignment length:220
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225
            RFP_DISSP     6 NVIKEFMRFKVRMEGTVNGHEFEIEGEGEGRPYEGHNTVKLKVTKGGPLPFAWDILSPQFQYGSKVYVKHPADIPDYKKLSFPEGFKWERVMNFEDGGVVTVTQDSSLQDGCFIYKVKFIGVNFPSDGPVMQKKTMGWEASTERLYPRDGVLKGEIHKALKLKDGGHYLVEFKSIYMAKKPVQLPGYYYVDSKLDITSHNEDYTIVEQYERTEGRHHLFL 225
               SCOP domains d1zgob_ B: automated matches                                                                                                                                                                                                 SCOP domains
               CATH domains 1zgoB00 B:6-225 Green Fluorescent Protein                                                                                                                                                                                    CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eeeeeeeeeee..eeeeeeeeeee.....eeeeeeeeee......hhhhhhhhh.--hhhhh.......hhhhhh....eeeeeeeee....eeeeeeeeeee..eeeeeeeeeee............eeee..eeeeeeee..eeeeeeeeeeee....eeeeeeeeeeee.........eeeeeeeeeeee.....eeeeeeeeeee..... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1zgo B   6 NVIKEFMRFKVRMEGTVNGHEFEIEGEGEGRPYEGHNTVKLKVTKGGPLPFAWDILSPQFq--SKVYVKHPADIPDYKKLSFPEGFKWERVMNFEDGGVVTVTQDSSLQDGCFIYKVKFIGVNFPSDGPVMQKKTMGWEASTERLYPRDGVLKGEIHKALKLKDGGHYLVEFKSIYMAKKPVQLPGYYYVDSKLDITSHNEDYTIVEQYERTEGRHHLFL 225
                                    15        25        35        45        55        65|  |    75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225
                                                                                       66-CRQ                                                                                                                                                           


Chain C from PDB  Type:PROTEIN  Length:218
 aligned with RFP_DISSP | Q9U6Y8 from UniProtKB/Swiss-Prot  Length:225

    Alignment length:220
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225
            RFP_DISSP     6 NVIKEFMRFKVRMEGTVNGHEFEIEGEGEGRPYEGHNTVKLKVTKGGPLPFAWDILSPQFQYGSKVYVKHPADIPDYKKLSFPEGFKWERVMNFEDGGVVTVTQDSSLQDGCFIYKVKFIGVNFPSDGPVMQKKTMGWEASTERLYPRDGVLKGEIHKALKLKDGGHYLVEFKSIYMAKKPVQLPGYYYVDSKLDITSHNEDYTIVEQYERTEGRHHLFL 225
               SCOP domains d1zgoc_ C: automated matches                                                                                                                                                                                                 SCOP domains
               CATH domains 1zgoC00 C:6-225 Green Fluorescent Protein                                                                                                                                                                                    CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eeeeeeeeeee..eeeeeeeeeeee....eeeeeeeeee......hhhhhhhhh.--hhhhh.......hhhhhh....eeeeeeeee....eeeeeeeeeee..eeeeeeeeeee............eeee..eeeeeeee..eeeeeeeeeeee....eeeeeeeeeeee.........eeeeeeeeeeee.....eeeeeeeeeee..... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1zgo C   6 NVIKEFMRFKVRMEGTVNGHEFEIEGEGEGRPYEGHNTVKLKVTKGGPLPFAWDILSPQFq--SKVYVKHPADIPDYKKLSFPEGFKWERVMNFEDGGVVTVTQDSSLQDGCFIYKVKFIGVNFPSDGPVMQKKTMGWEASTERLYPRDGVLKGEIHKALKLKDGGHYLVEFKSIYMAKKPVQLPGYYYVDSKLDITSHNEDYTIVEQYERTEGRHHLFL 225
                                    15        25        35        45        55        65|  |    75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225
                                                                                       66-CRQ                                                                                                                                                           


Chain D from PDB  Type:PROTEIN  Length:218
 aligned with RFP_DISSP | Q9U6Y8 from UniProtKB/Swiss-Prot  Length:225

    Alignment length:220
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225
            RFP_DISSP     6 NVIKEFMRFKVRMEGTVNGHEFEIEGEGEGRPYEGHNTVKLKVTKGGPLPFAWDILSPQFQYGSKVYVKHPADIPDYKKLSFPEGFKWERVMNFEDGGVVTVTQDSSLQDGCFIYKVKFIGVNFPSDGPVMQKKTMGWEASTERLYPRDGVLKGEIHKALKLKDGGHYLVEFKSIYMAKKPVQLPGYYYVDSKLDITSHNEDYTIVEQYERTEGRHHLFL 225
               SCOP domains d1zgod_ D: automated matches                                                                                                                                                                                                 SCOP domains
               CATH domains 1zgoD00 D:6-225 Green Fluorescent Protein                                                                                                                                                                                    CATH domains
           Pfam domains (1) GFP-1zgoD01 D:6-222                                                                                                                                                                                                      --- Pfam domains (1)
           Pfam domains (2) GFP-1zgoD02 D:6-222                                                                                                                                                                                                      --- Pfam domains (2)
           Pfam domains (3) GFP-1zgoD03 D:6-222                                                                                                                                                                                                      --- Pfam domains (3)
           Pfam domains (4) GFP-1zgoD04 D:6-222                                                                                                                                                                                                      --- Pfam domains (4)
         Sec.struct. author ......eeeeeeeeeee..eeeeeeeeeeee....eeeeeeeeee......hhhhhhhhh.--hhhhh.......hhhhhh....eeeeeeeee....eeeeeeeeeee..eeeeeeeeeee............eeee..eeeeeeee..eeeeeeeeeeee....eeeeeeeeeeee.........eeeeeeeeeeee.....eeeeeeeeeee..... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1zgo D   6 NVIKEFMRFKVRMEGTVNGHEFEIEGEGEGRPYEGHNTVKLKVTKGGPLPFAWDILSPQFq--SKVYVKHPADIPDYKKLSFPEGFKWERVMNFEDGGVVTVTQDSSLQDGCFIYKVKFIGVNFPSDGPVMQKKTMGWEASTERLYPRDGVLKGEIHKALKLKDGGHYLVEFKSIYMAKKPVQLPGYYYVDSKLDITSHNEDYTIVEQYERTEGRHHLFL 225
                                    15        25        35        45        55        65|  |    75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225
                                                                                       66-CRQ
   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  (3, 3)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B,C,D   (RFP_DISSP | Q9U6Y8)
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/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
    CRQ  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
(no "Sites" information available for 1zgo)
 
  Cis Peptide Bonds
    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 ]  
    Phe A:87 - Pro A:88   [ RasMol ]  
    Phe B:87 - Pro B:88   [ RasMol ]  
    Phe C:87 - Pro C:88   [ RasMol ]  
    Phe D:87 - Pro D:88   [ 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
  1zgo
    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
  RFP_DISSP | Q9U6Y8
    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
  RFP_DISSP | Q9U6Y8
    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
        RFP_DISSP | Q9U6Y8: 1g7k 1ggx 1zgp 1zgq 2h5o 2h5r 2h8q 2v4e 2vad 2vae 4i2y 4kf4 4kf5

(-) Related Entries Specified in the PDB File

1zgp CRYSTAL STRUCTURE OF THE DISCOSOMA RED FLUORESCENT PROTEIN (DSRED) VARIANT K70M
1zgq CRYSTAL STRUCTURE OF THE DISCOSOMA RED FLUORESCENT PROTEIN (DSRED) VARIANT Q66M