Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asymmetric Unit
(-)Biological Unit 1
(-)Biological Unit 2
collapse expand < >
Image Asymmetric Unit
Asymmetric Unit  (Jmol Viewer)
Image Biological Unit 1
Biological Unit 1  (Jmol Viewer)
Image Biological Unit 2
Biological Unit 2  (Jmol Viewer)

(-) Description

Title :  CRYSTAL STRUCTURE OF AMPHIOXUS GREEN FLUORESCENT PROTEIN, GFPA1
 
Authors :  E. K. Bomati, D. D. Deheyn
Date :  03 Feb 12  (Deposition) - 15 May 13  (Release) - 29 May 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.35
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (2x)
Biol. Unit 2:  A,B  (1x)
Keywords :  Chromophore, Beta-Can, Fluorescence, Fluorescent Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  E. K. Bomati, J. E. Haley, J. P. Noel, D. D. Deheyn
Fluorescent Proteins In Amphioxus Have Strickingly Differen Brightness, Yet Only Few (But Key) Molecular Differences
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - AMPHIOXUS GREEN FLUORESCENT PROTEIN, GFPA1
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PHIS8
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector: PET-LIKE
    Gene: BRAFLDRAFT_63256
    Organism Common: FLORIDA LANCELET
    Organism Scientific: BRANCHIOSTOMA FLORIDAE
    Organism Taxid: 7739

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric Unit (1, 2)
No.NameCountTypeFull Name
1CR22Mod. Amino Acid{(4Z)-2-(AMINOMETHYL)-4-[(4-HYDROXYPHENYL)METHYLIDENE]-5-OXO-4,5-DIHYDRO-1H-IMIDAZOL-1-YL}ACETIC ACID
Biological Unit 1 (1, 4)
No.NameCountTypeFull Name
1CR24Mod. Amino Acid{(4Z)-2-(AMINOMETHYL)-4-[(4-HYDROXYPHENYL)METHYLIDENE]-5-OXO-4,5-DIHYDRO-1H-IMIDAZOL-1-YL}ACETIC ACID
Biological Unit 2 (1, 2)
No.NameCountTypeFull Name
1CR22Mod. Amino Acid{(4Z)-2-(AMINOMETHYL)-4-[(4-HYDROXYPHENYL)METHYLIDENE]-5-OXO-4,5-DIHYDRO-1H-IMIDAZOL-1-YL}ACETIC ACID

(-) Sites  (0, 0)

(no "Site" information available for 4DKN)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (4, 4)

Asymmetric Unit
No.Residues
1Ile A:54 -Pro A:55
2Gln A:189 -Pro A:190
3Ile B:54 -Pro B:55
4Gln B:189 -Pro B:190

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4DKN)

(-) 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:210
 aligned with C3YKQ3_BRAFL | C3YKQ3 from UniProtKB/TrEMBL  Length:219

    Alignment length:218
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211        
         C3YKQ3_BRAFL     2 PLPATHDIHLHGSINGHEFDMVGGGKGDPNAGSLVTTAKSTKGALKFSPYLMIPHLGYGYYQYLPYPDGPSPFQTSMLEGSGYAVYRVFDFEDGGKLTTEFKYSYEGSHIKADMKLMGSGFPDDGPVMTSQIVDQDGCVSKKTYLNNNTIVDSFDWSYNLQNGKRYRARVSSHYIFDKPFSADLMKKQPVFVYRKCHVKASKTEVTLDEREKAFYELA 219
               SCOP domains d4dkna_ A: automated matches                                                                                                                                                                                               SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeeeeeee..eeeeeeeeeee......eeeeeee.......hhhhhh...--.hhhh.ee..eehhhhhhhhh...eeeeeeeee....eeeeeeeeeee..eeeeeeeeeee............eeee..eeeeeeee...eeeeeeeeeeee....eeeeeeeeeeee....------...eeeeeeeeeee...eeeeeeeeeee.... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4dkn A   2 PLPATHDIHLHGSINGHEFDMVGGGKGDPNAGSLVTTAKSTKGALKFSPYLMIPHL--gYYQYLPYPDGPSPFQVSMLEGSGYAVYRVFDFEDGGKLSTEFKYSYEGSHIKADMKLMGSGFPDDGPVMTSQIVDQDGCVSKKTYLNNNTIVDSFDWSYNLQNGKRYRARVSSHYIFDKPF------KQPVFVYRKCHVKATKTEVTLDEREKAFYELA 219
                                    11        21        31        41        51     |  61        71        81        91       101       111       121       131       141       151       161       171       181      |191       201       211        
                                                                                  57  |                                                                                                                      181    188                               
                                                                                     60-CR2                                                                                                                                                           


Chain B from PDB  Type:PROTEIN  Length:215
 aligned with C3YKQ3_BRAFL | C3YKQ3 from UniProtKB/TrEMBL  Length:219

    Alignment length:217
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       
         C3YKQ3_BRAFL     2 PLPATHDIHLHGSINGHEFDMVGGGKGDPNAGSLVTTAKSTKGALKFSPYLMIPHLGYGYYQYLPYPDGPSPFQTSMLEGSGYAVYRVFDFEDGGKLTTEFKYSYEGSHIKADMKLMGSGFPDDGPVMTSQIVDQDGCVSKKTYLNNNTIVDSFDWSYNLQNGKRYRARVSSHYIFDKPFSADLMKKQPVFVYRKCHVKASKTEVTLDEREKAFYEL 218
               SCOP domains d4dknb_ B: automated matches                                                                                                                                                                                              SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeeeeeee..eeeeeeeeeeee....eeeeeeee.......hhhhhh...--.hhhh.ee..eehhhhhhhhh...eeeeeeeee....eeeeeeeeeee..eeeeeeeeeee............eeee..eeeeeeee...eeeeeeeeeeee....eeeeeeeeeeee......hhhhh..eeeeeeeeeee...eeeeeeeeeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4dkn B   2 PLPATHDIHLHGSINGHEFDMVGGGKGDPNAGSLVTTAKSTKGALKFSPYLMIPHL--gYYQYLPYPDGPSPFQVSMLEGSGYAVYRVFDFEDGGKLSTEFKYSYEGSHIKADMKLMGSGFPDDGPVMTSQIVDQDGCVSKKTYLNNNTIVDSFDWSYNLQNGKRYRARVSSHYIFDKPFSADLMKKQPVFVYRKCHVKATKTEVTLDEREKAFYEL 218
                                    11        21        31        41        51     |  61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       
                                                                                  57  |                                                                                                                                                              
                                                                                     60-CR2
   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 4DKN)

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (1, 1)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (C3YKQ3_BRAFL | C3YKQ3)
biological process
    GO:0008218    bioluminescence    The production of light by certain enzyme-catalyzed reactions in cells.

 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
    CR2  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
(no "Sites" information available for 4dkn)
 
  Cis Peptide Bonds
    Gln A:189 - Pro A:190   [ RasMol ]  
    Gln B:189 - Pro B:190   [ RasMol ]  
    Ile A:54 - Pro A:55   [ RasMol ]  
    Ile B:54 - Pro B:55   [ 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 | Biol. Unit 1 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
  4dkn
    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
  C3YKQ3_BRAFL | C3YKQ3
    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
  C3YKQ3_BRAFL | C3YKQ3
    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 4DKN)

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 4DKN)