Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asym.Unit - manually
(-)Asymmetric Unit
(-)Biological Unit 1
(-)Biological Unit 2
collapse expand < >
Image Asym.Unit - manually
Asym.Unit - manually  (Jmol Viewer)
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 :  PREDICTED CODING REGION AF1432 FROM ARCHAEOGLOBUS FULGIDUS
 
Authors :  Midwest Center For Structural Genomics (Mcsg), V. V. Lunin, A. Sa A. Joachimiak
Date :  28 Jan 05  (Deposition) - 08 Feb 05  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Biol. Unit 2:  A  (6x)
Keywords :  Af1432, Apc5594, Midwest Center For Structural Genomics, Mcsg, Protein Structure Initiative, Psi, Structural Genomics, Unknown Function (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  V. V. Lunin, E. Evdokimova, M. Kudritskaya, A. Joachimiak, A. Edwards A. Savchenko
The Crystal Structure Of Predicted Coding Region Af1432 Fro Archaeoglobus Fulgidus
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - HYPOTHETICAL PROTEIN AF1432
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI BL21(DE3)
    Expression System PlasmidMODIFIED PET15B
    Expression System StrainBL21 DE3
    Expression System Taxid469008
    Expression System Vector TypePLASMID
    Organism ScientificARCHAEOGLOBUS FULGIDUS
    Organism Taxid224325
    StrainDSM 4304

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit A
Biological Unit 1 (2x)A
Biological Unit 2 (6x)A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 1YOY)

(-) Sites  (0, 0)

(no "Site" information available for 1YOY)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1YOY)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 1YOY)

(-) 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:146
 aligned with O28840_ARCFU | O28840 from UniProtKB/TrEMBL  Length:173

    Alignment length:166
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166      
         O28840_ARCFU     7 MDDVVKFIHEVGSLKLTPRSGWLKLGIRLPESVAEHSFRAAIIAFILALKSGESVEKACKAATAALFHDLHEARTMDLHKIARRYVSCDEEGAREEQLSWMESKPDFSDVEVYVSDADKLELAFQGVEYSQQVSYAIRFAENVELKTDAAKEIYRVLMERKNPVWW 172
               SCOP domains d1yoya1 A:7-172 Hypothetical protein AF1432                                                                                                                            SCOP domains
               CATH domains 1yoyA00 A:7-172 Hypothetical protein af1432                                                                                                                            CATH domains
               Pfam domains --------------------------------HD-1yoyA01 A:39-129                                                                        ------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhh.hhhhhhhh.....hhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhh--------------------hhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1yoy A   7 MDDVVKFIHEVGSLKLTPRSGWLKLGIRLPESVAEHSFRAAIIAFILALKSGESVEKACKAATAALFHDLHEAR--------------------EEQLSWMESKPDFSDVEVYVSDADKLELAFQGVEYSQQVSYAIRFAENVELKTDAAKEIYRVLMERKNPVWW 172
                                    16        26        36        46        56        66        76   |     -         -    |  106       116       126       136       146       156       166      
                                                                                                    80                  101                                                                       

   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, 1)

Asymmetric Unit

(-) CATH Domains  (1, 1)

Asymmetric Unit

(-) Pfam Domains  (1, 1)

Asymmetric Unit

(-) Gene Ontology  (0, 0)

Asymmetric Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 1YOY)

 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
(no "Ligands, Modified Residues, Ions" information available for 1yoy)
 
  Sites
(no "Sites" information available for 1yoy)
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 1yoy)
 
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
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  1yoy
    Family and Domain InformationProDom | SYSTERS
    General Structural InformationGlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in MembranesOPM
    Protein SurfaceSURFACE
    Secondary StructureDSSP (structure derived) | HSSP (homology derived)
    Structural GenomicsGeneCensus
    Structural NeighboursCE | VAST
    Structure ClassificationCATH | Dali | SCOP
    Validation and Original DataBMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  O28840_ARCFU | O28840
    Comparative Protein Structure ModelsModBase
    Genomic InformationEnsembl
    Protein-protein InteractionDIP
    Sequence, Family and Domain InformationInterPro | Pfam | SMART | UniProtKB/TrEMBL
 
Access by Enzyme Classificator   (EC Number)
  (no 'Enzyme Classificator' available)
    General Enzyme InformationBRENDA | EC-PDB | Enzyme | IntEnz
    PathwayKEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease InformationOMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related InformationGenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain InformationXDom
    Interatomic Contacts of Structural UnitsCSU
    Ligand-protein ContactsLPC
    Protein CavitiescastP
    Sequence and Secondary StructurePDBCartoon
    Structure AlignmentSTRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence BrowserSTING
 
Access by UniProt ID/Accession number
  O28840_ARCFU | O28840
    Protein Disorder PredictionDisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/TrEMBL
        O28840_ARCFU | O288401ynb

(-) Related Entries Specified in the PDB File

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