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
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)

(-) Description

Title :  CRYSTAL STRUCTURE OF RED FLUORESCENT GENE-ENGINEERED VARIANT WITH IMPROVED FOLDING - LANRFP_DELS83 (BRANCHIOSTOMA LANCEOLATUM)
 
Authors :  V. Z. Pletnev, N. V. Pletneva, S. V. Pletnev
Date :  01 Mar 13  (Deposition) - 18 Sep 13  (Release) - 18 Sep 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.94
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (2x)
Keywords :  Lanrfp, Fluoresent Proteins, Beta-Barrel, Gly-Tyr-Gly Chromophore, Cephalochordate, Fluorescent Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  V. Z. Pletnev, N. V. Pletneva, K. A. Lukyanov, E. A. Souslova, A. F. Fradkov, D. M. Chudakov, T. Chepurnykh, I. V. Yampolsky, A. Wlodawer, Z. Dauter, S. Pletnev
Structure Of The Red Fluorescent Protein From A Lancelet (Branchiostoma Lanceolatum): A Novel Gyg Chromophore Covalently Bound To A Nearby Tyrosine.
Acta Crystallogr. , Sect. D V. 69 1850 2013
PubMed-ID: 23999308  |  Reference-DOI: 10.1107/S0907444913015424

(-) Compounds

Molecule 1 - RED FLUORESCENT PROTEIN BLFP-R5
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PQE30
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: BLFP-R5
    Mutation: YES
    Organism Common: COMMON LANCELET
    Organism Scientific: BRANCHIOSTOMA LANCEOLATUM
    Organism Taxid: 7740

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (2, 3)
No.NameCountTypeFull Name
1CR22Mod. Amino Acid{(4Z)-2-(AMINOMETHYL)-4-[(4-HYDROXYPHENYL)METHYLIDENE]-5-OXO-4,5-DIHYDRO-1H-IMIDAZOL-1-YL}ACETIC ACID
2GOL1Ligand/IonGLYCEROL
Biological Unit 1 (2, 6)
No.NameCountTypeFull Name
1CR24Mod. Amino Acid{(4Z)-2-(AMINOMETHYL)-4-[(4-HYDROXYPHENYL)METHYLIDENE]-5-OXO-4,5-DIHYDRO-1H-IMIDAZOL-1-YL}ACETIC ACID
2GOL2Ligand/IonGLYCEROL

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLU A:94 , GLN A:169 , HOH A:443 , HOH A:605 , HOH A:607 , ASP B:95 , LYS B:155 , HOH B:515BINDING SITE FOR RESIDUE GOL A 301

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (4, 4)

Asymmetric Unit
No.Residues
1Val A:54 -Pro A:55
2Gln A:190 -Pro A:191
3Val B:54 -Pro B:55
4Gln B:190 -Pro B:191

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4JGE)

(-) 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:216
                                                                                                                                                                                                                                                        
               SCOP domains d4jgea_ A: automated matches                                                                                                                                                                                             SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .....eeeeeeeeee..eeeeeeeeeee......eeeeeee.......hhhhhh....hhhhh.hhhhh.hhhhhhhh...eeeeeeeee....eeeeeeeeeee..eeeeeeeeeee............eeee..eeeeeeeee..eeeeeeeeeeee.....eeeeeeeeeee....hhhhhh...eeeeeeeeeee...eeeeeeeeeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4jge A   1 SPLPATHDLHISGSINGHEFDLEGSGKGNAKEGYQELHLKSNKGDLSFSPWILVPNIgFYQYLPFPDGAMSPYQAAMHDGGYVMHRSMQFEDGAMLHSDHRYIYKGNHIKGEFRLTGSGFPADGPVMTNSLTAADWCVDKLLYPNDNTIIGKFDWTYTTTSGKRYQSDVQTNVTFGKPIAADILKKQPMFVFRKVELKHTKTELNFKQWQKAFQDI 219
                                    10        20        30        40        50       |62        72        82|       93       103       113       123       133       143       153       163       173       183       193       203       213      
                                                                                    58-CR2                82|                                                                                                                                       
                                                                                     61                    84                                                                                                                                       


Chain B from PDB  Type:PROTEIN  Length:217
                                                                                                                                                                                                                                                         
               SCOP domains d4jgeb_ B: automated matches                                                                                                                                                                                              SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeeeeeeee..eeeeeeeeeeee....eeeeeeee.......hhhhhh....hhhhh.hhhhh.hhhhhhhh...eeeeeeeee....eeeeeeeeeee..eeeeeeeeeee............eeee..eeeeeeeee..eeeeeeeeeeee.....eeeeeeeeeee....hhhhhh...eeeeeeeeeee...eeeeeeeeeee.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4jge B   1 SPLPATHDLHISGSINGHEFDLEGSGKGNAKEGYQELHLKSNKGDLSFSPWILVPNIgFYQYLPFPDGAMSPYQAAMHDGGYVMHRSMQFEDGAMLHSDHRYIYKGNHIKGEFRLTGSGFPADGPVMTNSLTAADWCVDKLLYPNDNTIIGKFDWTYTTTSGKRYQSDVQTNVTFGKPIAADILKKQPMFVFRKVELKHTKTELNFKQWQKAFQDIA 220
                                    10        20        30        40        50       |62        72        82|       93       103       113       123       133       143       153       163       173       183       193       203       213       
                                                                                    58-CR2                82|                                                                                                                                        
                                                                                     61                    84
   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 4JGE)

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (1, 1)

Asymmetric Unit(hide GO term definitions)

 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 ]
    GOL  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Gln A:190 - Pro A:191   [ RasMol ]  
    Gln B:190 - Pro B:191   [ RasMol ]  
    Val A:54 - Pro A:55   [ RasMol ]  
    Val B:54 - Pro B:55   [ RasMol ]  
 
Biological Unit
  Complete Structure
    Biological Unit 1  [ 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 ](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
  4jge
    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
  B1PND0_BRALA | B1PND0
    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
  B1PND0_BRALA | B1PND0
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/TrEMBL
        B1PND0_BRALA | B1PND0: 4jeo 4jf9

(-) Related Entries Specified in the PDB File

2dd7 MARINE COPEPOD (CHIRIDIUS POPPEI)
2g3o WILD TYPE GREEN FLUORESCENT PROTEIN COPGFP (PONTELLIDAE PLUMATA)
4hvf WILD TYPE GREEN FLUORESCENT PROTEIN LANGFP (BRANCHIOSTOMA LANCEOLATUM)
4jeo
4jf9 WILD TYPE RED FLUORESCENT PROTEIN LANRFP (BRANCHIOSTOMA LANCEOLATUM)