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

(-) Description

Title :  N-TERMINAL COILED-COIL DIMER OF C.ELEGANS SAS-6, CRYSTAL FORM B
 
Authors :  M. C. Erat, I. Vakonakis
Date :  03 Aug 12  (Deposition) - 19 Jun 13  (Release) - 24 Jul 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.85
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Beta-Sandwich, Alpha-Beta Protein, Structural Protein, Cytoplasmic, Centriolar, Central Tube (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. Hilbert, M. C. Erat, V. Hachet, P. Guichard, I. D. Blank, I. Fluckiger, L. Slater, E. D. Lowe, G. N. Hatzopoulos, M. O. Steinmetz P. Gonczy, I. Vakonakis
Caenorhabditis Elegans Centriolar Protein Sas-6 Forms A Spiral That Is Consistent With Imparting A Ninefold Symmetry.
Proc. Natl. Acad. Sci. Usa V. 110 11373 2013
PubMed-ID: 23798409  |  Reference-DOI: 10.1073/PNAS.1302721110

(-) Compounds

Molecule 1 - SPINDLE ASSEMBLY ABNORMAL PROTEIN 6
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: MODIFIED PET15B
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: SAS-6 N-TERMINAL HEAD DOMAIN AND BEGINNING OF COILED COIL
    Gene: SAS-6, Y45F10D.9
    Mutation: YES
    Organism Common: NEMATODE
    Organism Scientific: CAENORHABDITIS ELEGANS
    Organism Taxid: 6239

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 12)

Asymmetric/Biological Unit (3, 12)
No.NameCountTypeFull Name
1EDO8Ligand/Ion1,2-ETHANEDIOL
2IMD2Ligand/IonIMIDAZOLE
3PG42Ligand/IonTETRAETHYLENE GLYCOL

(-) Sites  (12, 12)

Asymmetric Unit (12, 12)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREALA A:6 , ASP A:9 , EDO A:210BINDING SITE FOR RESIDUE EDO A 201
02AC2SOFTWAREASP A:26 , PHE A:27 , VAL A:85 , VAL A:93 , HIS A:97 , HOH A:330BINDING SITE FOR RESIDUE EDO A 202
03AC3SOFTWAREGLU A:40 , PHE A:87 , ASP A:88 , PRO A:91BINDING SITE FOR RESIDUE EDO A 203
04AC4SOFTWARELEU A:12 , LEU A:98 , CYS A:100 , THR A:103 , ILE A:105 , PG4 A:208BINDING SITE FOR RESIDUE EDO A 204
05AC5SOFTWAREPHE A:27 , HIS A:97 , CYS A:100 , SER A:122 , THR A:124BINDING SITE FOR RESIDUE IMD A 205
06AC6SOFTWARELYS A:52 , HIS A:137 , VAL A:139 , HIS A:143BINDING SITE FOR RESIDUE IMD A 206
07AC7SOFTWARELYS A:92 , GLN A:96 , GLU A:104 , ASN A:106 , GLU A:119BINDING SITE FOR RESIDUE PG4 A 207
08AC8SOFTWAREILE A:13 , LYS A:101 , EDO A:204BINDING SITE FOR RESIDUE PG4 A 208
09AC9SOFTWAREARG A:57 , HOH A:306BINDING SITE FOR RESIDUE EDO A 209
10BC1SOFTWARELEU A:7 , PHE A:8 , ASP A:9 , GLN A:10 , EDO A:201BINDING SITE FOR RESIDUE EDO A 210
11BC2SOFTWAREHIS A:81 , LYS A:128BINDING SITE FOR RESIDUE EDO A 211
12BC3SOFTWARELEU B:83 , VAL B:85BINDING SITE FOR RESIDUE EDO B 201

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4GFC)

(-) 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:165
                                                                                                                                                                                                     
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeeeeeeeeeeeee..eeeeeeeeeeeeeeeeeee...eeeeeeeee..eeeeeeeeeehhhhhhhhhhhhh......hhhhhhhhhhhh..eeeeeee.....eeeeeeee.......eeeeeeeee.hhhhhhhhhhhhhhhhhhhhhhh.hhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4gfc A   2 TSKIALFDQTLIASLLQPLSLNQPDFKAYKTKVKLKISEQRNEEKELKFEISRSDDFEFLFSETLNNEKYQILARDHDLTVDFDAFPKVIIQHLLCKNTEINIILDAEKNFCSFELFSKTPGSKGKIFSIKLHAVRGDHLISHLLKICSSQAVKLSTFKSADELA 170
                                    11        21        31        41  ||    54        64        74        84        94       104       114       124       134       144       154       165     
                                                                     44|                                                                                                               162|      
                                                                      48                                                                                                                164      


Chain B from PDB  Type:PROTEIN  Length:151
                                                                                                                                                                                       
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeeeeeeeee....eeeeeeeeeeee....eeeeee..eeeeeeeee.hhhhhhhhhhhh.......hhhhhhhhhhhh.....eeee.....eee...eee.hhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4gfc B   3 SKIALFDQTLIASLLQPKAYKTKVKLKISEQRNELKFEISRSDDFEFLFSETLNNEKYQILARDHDLTVDFDAFPKVIIQHLLCKNTEINIILDAEKNFCSFIKLHAVRGDHLISHLLKICSSQAVKLSTFYKSADELASLRQKCGDLEKQ 182
                                    12      ||30        40   ||   56        66        76        86        96       106       116 ||    141       151       161       171       181 
                                           19|              44|                                                                118|                                                
                                            28               51                                                                 134
   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 4GFC)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (11, 11)

Asymmetric/Biological Unit(hide GO term definitions)

 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
    EDO  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    IMD  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    PG4  [ 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 ]
    AC6  [ RasMol ]  +environment [ RasMol ]
    AC7  [ RasMol ]  +environment [ RasMol ]
    AC8  [ RasMol ]  +environment [ RasMol ]
    AC9  [ RasMol ]  +environment [ RasMol ]
    BC1  [ RasMol ]  +environment [ RasMol ]
    BC2  [ RasMol ]  +environment [ RasMol ]
    BC3  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 4gfc)
 

(-) 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
  4gfc
    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
  SAS6_CAEEL | O62479
    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
  SAS6_CAEEL | O62479
    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
        SAS6_CAEEL | O62479: 3pyi 4g79 4geu 4gex 4gfa 4gkw

(-) Related Entries Specified in the PDB File

2y3v N-TERMINAL HEAD DOMAIN OF DANIO RERIO SAS-6
2y3w N-TERMINAL HEAD DOMAIN AND BEGINNING OF COILED COIL DOMAIN OF DANIO RERIO SAS-6
3pyi STRUCTURE OF THE N-TERMINAL DOMAIN OF C.ELEGANS SAS-6
3q0x N-TERMINAL COILED-COIL DIMER DOMAIN OF C.RINHARDTII SAS-6 HOMOLOG BLD12P
3q0y N-TERMINAL DOMAIN OF C.REINHARDTII SAS-6 HOMOLOG BLD12P
4g79 STRUCTURE A C. ELEGANS SAS-6 VARIANT
4geu STRUCTURE OF A STABILISED CESAS-6 DIMER
4gex STRUCTURE OF A STABILISED CESAS-6 DIMER, SECOND CRYSTAL FORM
4gfa N-TERMINAL COILED-COIL DIMER OF C.ELEGANS SAS-6, CRYSTAL FORM A