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
(-)Asym./Biol. Unit - sites
collapse expand < >
Image Asym./Biol. Unit - manually
Asym./Biol. Unit - manually  (Jmol Viewer)
Image Asym./Biol. Unit
Asym./Biol. Unit  (Jmol Viewer)
Image Asym./Biol. Unit - sites
Asym./Biol. Unit - sites  (Jmol Viewer)

(-) Description

Title :  SEMI-RATIONAL ENGINEERING OF A GREEN-EMITTING CORAL FLUORESCENT PROTEIN INTO AN EFFICIENT HIGHLIGHTER.
 
Authors :  H. Tsutsui, S. Karasawa, H. Shimizu, N. Nukina, A. Miyawaki
Date :  20 Oct 04  (Deposition) - 15 Mar 05  (Release) - 16 Nov 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.60
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Fluorescent Protein, Luminescent Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  H. Tsutsui, S. Karasawa, H. Shimizu, N. Nukina, A. Miyawaki
Semi-Rational Engineering Of A Coral Fluorescent Protein Into An Efficient Highlighter
Embo Rep. V. 6 233 2005
PubMed-ID: 15731765  |  Reference-DOI: 10.1038/SJ.EMBOR.7400361

(-) Compounds

Molecule 1 - FLUORESCENT PROTEIN
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Organism Scientific: FAVIA FAVUS
    Organism Taxid: 102203

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 6)

Asymmetric/Biological Unit (3, 6)
No.NameCountTypeFull Name
1DYG2Mod. Amino Acid(3S)-3-AMINO-3-[(4Z)-1-(CARBOXYMETHYL)-4-[(4-HYDROXYPHENYL)METHYLIDENE]-5-OXO-IMIDAZOL-2-YL]PROPANOIC ACID
2MG2Ligand/IonMAGNESIUM ION
3NA2Ligand/IonSODIUM ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETYR A:207 , HOH A:1356 , HOH A:1364 , HOH A:1442 , HOH A:1448BINDING SITE FOR RESIDUE MG A 1300
2AC2SOFTWAREVAL A:76 , ASP A:190BINDING SITE FOR RESIDUE NA A 1301
3AC3SOFTWARETYR B:207 , HOH B:2348 , HOH B:2353 , HOH B:2389 , HOH B:2432 , HOH B:2459BINDING SITE FOR RESIDUE MG B 2300
4AC4SOFTWAREVAL B:76 , ASP B:190 , HOH B:2521BINDING SITE FOR RESIDUE NA B 2301

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1Gly A:48 -Pro A:49
2Phe A:83 -Pro A:84
3Gly B:48 -Pro B:49
4Phe B:83 -Pro B:84

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 1XSS)

(-) 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 Q53UG7_FAVFA | Q53UG7 from UniProtKB/TrEMBL  Length:227

    Alignment length:226
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220      
         Q53UG7_FAVFA     1 MSVITSEMKMELRMEGAVNGHKFVITGKGSGQPFEGIQNMDLTVIEGGPLPFAFDILTTVFDYGNRVFVKYPEEIVDYFKQSFPEGYSWERSMSYEDGGICLATNNITMKKDGSNCFVYEIRFDGVNFPANGPVMQRKTVKWEPSTEKMYVRDGVLKGDVNMALLLQGGGHYRCDFRTTYKAKKVVQLPDYHFVDHRIEITSHDKDYNKVKLYEHAKAHSGLPRLA 226
               SCOP domains d1xssa_ A: automated matches                                                                                                                                                                                                       SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eeeeeeeeeee..eeeeeeeeeeee....eeeeeeeeee.......hhhhhh..--.............hhhhhhh...eeeeeeeee....eeeeeeeeee......eeeeeeeeeee............eeee..eeeeeeee..eeeeeeeeeeee....eeeeeeeeeeee.........eeeeeeeeeeee.....eeeeeeeeeee....... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1xss A   1 VSVITSEMKMELRMEGAVNGHKFVITGKGSGQPFEGIQNMDLTVIEGGPLPFAFDILTTVF--dNRVFVKYPEEIVDYFKQSFPEGYSWERSMSYEDGGICLATNNITMKKDGSNCFVYEIRFDGVNFPANGPVMQRKTVKWEPSTEKMYVRDGVLKGDVNMALLLQGGGHYRCDFRTTYKAKKVVQLPDYHFVDHRIEITSHDKDYNKVKLYEHAKAHSGLPRLA 226
                                    10        20        30        40        50        60|  |    70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220      
                                                                                       61  |                                                                                                                                                                  
                                                                                          64-DYG                                                                                                                                                              


Chain B from PDB  Type:PROTEIN  Length:225
 aligned with Q53UG7_FAVFA | Q53UG7 from UniProtKB/TrEMBL  Length:227

    Alignment length:227
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       
         Q53UG7_FAVFA     1 MSVITSEMKMELRMEGAVNGHKFVITGKGSGQPFEGIQNMDLTVIEGGPLPFAFDILTTVFDYGNRVFVKYPEEIVDYFKQSFPEGYSWERSMSYEDGGICLATNNITMKKDGSNCFVYEIRFDGVNFPANGPVMQRKTVKWEPSTEKMYVRDGVLKGDVNMALLLQGGGHYRCDFRTTYKAKKVVQLPDYHFVDHRIEITSHDKDYNKVKLYEHAKAHSGLPRLAK 227
               SCOP domains d1xssb_ B: automated matches                                                                                                                                                                                                        SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eeeeeeeeeee..eeeeeeeeeeee....eeeeeeeeee.......hhhhhh..--.............hhhhhhh...eeeeeeeee....eeeeeeeeee......eeeeeeeeeee............eeee..eeeeeeee..eeeeeeeeeeee....eeeeeeeeeeee.........eeeeeeeeeeee.....eeeeeeeeeee........ Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1xss B   1 VSVITSEMKMELRMEGAVNGHKFVITGKGSGQPFEGIQNMDLTVIEGGPLPFAFDILTTVF--dNRVFVKYPEEIVDYFKQSFPEGYSWERSMSYEDGGICLATNNITMKKDGSNCFVYEIRFDGVNFPANGPVMQRKTVKWEPSTEKMYVRDGVLKGDVNMALLLQGGGHYRCDFRTTYKAKKVVQLPDYHFVDHRIEITSHDKDYNKVKLYEHAKAHSGLPRLAK 227
                                    10        20        30        40        50        60|  |    70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       
                                                                                       61  |                                                                                                                                                                   
                                                                                          64-DYG
   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/Biological Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 1XSS)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1XSS)

(-) Gene Ontology  (1, 1)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (Q53UG7_FAVFA | Q53UG7)
biological process
    GO:0008218    bioluminescence    The production of light by certain enzyme-catalyzed reactions in cells.

 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
    DYG  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    MG  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    NA  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
    AC4  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Gly A:48 - Pro A:49   [ RasMol ]  
    Gly B:48 - Pro B:49   [ RasMol ]  
    Phe A:83 - Pro A:84   [ RasMol ]  
    Phe B:83 - Pro B:84   [ 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 | 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
  1xss
    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
  Q53UG7_FAVFA | Q53UG7
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/TrEMBL
 
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
  Q53UG7_FAVFA | Q53UG7
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

(no "Entries Sharing at Least One Protein Chain" available for 1XSS)

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 1XSS)