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
(-)Biological Unit 2
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)
Image Biological Unit 2
Biological Unit 2  (Jmol Viewer)

(-) Description

Title :  COILED COIL DOMAIN OF THE ZFL2-1 ORF1 PROTEIN FROM THE ZEBRAFISH ZFL2-1 RETROTRANSPOSON
 
Authors :  A. M. Schneider, O. Weichenrieder
Date :  11 Aug 13  (Deposition) - 11 Sep 13  (Release) - 25 Dec 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.55
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
Keywords :  Hydrolase, Retrotransposition, Rna-Binding, Membrane-Binding, Lipid-Binding, Self-Association (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. M. Schneider, S. Schmidt, S. Jonas, B. Vollmer, E. Khazina, O. Weichenrieder
Structure And Properties Of The Esterase From Non-Ltr Retrotransposons Suggest A Role For Lipids In Retrotransposition.
Nucleic Acids Res. V. 41 10563 2013
PubMed-ID: 24003030  |  Reference-DOI: 10.1093/NAR/GKT786

(-) Compounds

Molecule 1 - ORF1-ENCODED PROTEIN
    Chains: A, B, C, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PETM60
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Variant: STAR
    Fragment: COILED COIL DOMAIN, RESIDUES 15-47
    Organism Common: ZEBRAFISH
    Organism Scientific: DANIO RERIO
    Organism Taxid: 7955
    Other Details: SYNTHETIC CODON-OPTIMIZED DNA SEQUENCE
    Synonym: ZFL2-1 ORF1P

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): AB  
Biological Unit 2 (1x):   CD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 5)

Asymmetric Unit (1, 5)
No.NameCountTypeFull Name
1GOL5Ligand/IonGLYCEROL
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1GOL1Ligand/IonGLYCEROL
Biological Unit 2 (1, 4)
No.NameCountTypeFull Name
1GOL4Ligand/IonGLYCEROL

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREILE A:29 , ARG A:36 , HOH A:2033 , VAL B:33 , ARG B:36 , GLU C:24 , GLU D:24BINDING SITE FOR RESIDUE GOL A1048
2AC2SOFTWAREVAL D:33 , ARG D:36 , SER D:37 , ARG D:40 , GOL D:1047BINDING SITE FOR RESIDUE GOL D1046
3AC3SOFTWAREILE C:29 , VAL D:33 , ARG D:36 , GOL D:1046 , HOH D:2023 , HOH D:2030BINDING SITE FOR RESIDUE GOL D1047
4AC4SOFTWAREVAL C:33 , ARG C:36 , SER C:37 , ARG C:40 , GOL C:1048BINDING SITE FOR RESIDUE GOL C1047
5AC5SOFTWAREVAL C:33 , ARG C:36 , GOL C:1047 , ILE D:29BINDING SITE FOR RESIDUE GOL C1048

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4C1A)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4C1A)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4C1A)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4C1A)

(-) Exons   (0, 0)

(no "Exon" information available for 4C1A)

(-) 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:36
 aligned with Q3LG57_DANRE | Q3LG57 from UniProtKB/TrEMBL  Length:302

    Alignment length:37
                                    20        30        40       
          Q3LG57_DANRE   11 GEASMEALELELEEVESQIRALVVRRSRLRERLLAVP 47
               SCOP domains ------------------------------------- SCOP domains
               CATH domains ------------------------------------- CATH domains
               Pfam domains ------------------------------------- Pfam domains
         Sec.struct. author .hh-hhhhhhhhhhhhhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------- PROSITE
                 Transcript ------------------------------------- Transcript
                  4c1a A 12 GPA-MEALELELEEVESQIRALVVRRSRLRERLLAVP 47
                              | |   20        30        40       
                             14 |                                
                               15                                


Chain B from PDB  Type:PROTEIN  Length:35
 aligned with Q3LG57_DANRE | Q3LG57 from UniProtKB/TrEMBL  Length:302

    Alignment length:36
                                    20        30        40      
          Q3LG57_DANRE   11 GEASMEALELELEEVESQIRALVVRRSRLRERLLAV 46
               SCOP domains ------------------------------------ SCOP domains
               CATH domains ------------------------------------ CATH domains
               Pfam domains ------------------------------------ Pfam domains
         Sec.struct. author .hh-hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------ PROSITE
                 Transcript ------------------------------------ Transcript
                  4c1a B 12 GPA-MEALELELEEVESQIRALVVRRSRLRERLLAV 46
                              | |   20        30        40      
                             14 |                               
                               15                               


Chain C from PDB  Type:PROTEIN  Length:35
 aligned with Q3LG57_DANRE | Q3LG57 from UniProtKB/TrEMBL  Length:302

    Alignment length:36
                                    20        30        40      
          Q3LG57_DANRE   11 GEASMEALELELEEVESQIRALVVRRSRLRERLLAV 46
               SCOP domains ------------------------------------ SCOP domains
               CATH domains ------------------------------------ CATH domains
               Pfam domains ------------------------------------ Pfam domains
         Sec.struct. author .hh-hhhhhhhhhhhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------ PROSITE
                 Transcript ------------------------------------ Transcript
                  4c1a C 12 GPA-MEALELELEEVESQIRALVVRRSRLRERLLAV 46
                              | |   20        30        40      
                             14 |                               
                               15                               


Chain D from PDB  Type:PROTEIN  Length:32
 aligned with Q3LG57_DANRE | Q3LG57 from UniProtKB/TrEMBL  Length:302

    Alignment length:32
                                    23        33        43  
          Q3LG57_DANRE   14 SMEALELELEEVESQIRALVVRRSRLRERLLA 45
               SCOP domains -------------------------------- SCOP domains
               CATH domains -------------------------------- CATH domains
               Pfam domains -------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------- PROSITE
                 Transcript -------------------------------- Transcript
                  4c1a D 14 AMEALELELEEVESQIRALVVRRSRLRERLLA 45
                                    23        33        43
   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  (0, 0)

(no "SCOP Domain" information available for 4C1A)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4C1A)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4C1A)

(-) Gene Ontology  (0, 0)

Asymmetric Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 4C1A)

 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
    GOL  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
    AC4  [ RasMol ]  +environment [ RasMol ]
    AC5  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 4c1a)
 
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 | Asym. Unit - sites PNG format | Biol. Unit 1 PNG format | Biol. Unit 1 - sites 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
  4c1a
    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
  Q3LG57_DANRE | Q3LG57
    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
  Q3LG57_DANRE | Q3LG57
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/TrEMBL
        Q3LG57_DANRE | Q3LG57: 4c1b

(-) Related Entries Specified in the PDB File

4c1b ESTERASE DOMAIN OF THE ZFL2-1 ORF1 PROTEIN FROM THE ZEBRAFISH ZFL2-1 RETROTRANSPOSON