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

(-) Description

Title :  X-RAY STRUCTURE OF GENE PRODUCT FROM ARABIDOPSIS THALIANA AT5G48480
 
Authors :  G. E. Wesenberg, G. N. Phillips Jr. , E. Bitto, C. A. Bingman, S. T. M. Allard, Center For Eukaryotic Structural Genomics (Cesg)
Date :  09 Nov 04  (Deposition) - 16 Nov 04  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Structural Genomics, Protein Structure Initiative, Psi, Cesg, At5G48480, Reductively Methylated Protein, Cath 3. 10. 180 Fold, Unknown Function, Dimer, Center For Eukaryotic Structural Genomics (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Center For Eukaryotic Structural Genomics (Cesg)
X-Ray Structure Of Gene Product From Arabidopsis Thaliana At5G48480
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - UNKNOWN PROTEIN
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PVP-13
    Expression System Strain: B834(DE3) P(LACI+RARE)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: AT5G48480
    Organism Common: THALE CRESS
    Organism Scientific: ARABIDOPSIS THALIANA
    Organism Taxid: 3702

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (1, 2)
No.NameCountTypeFull Name
1MSE2Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (0, 0)

(no "Site" information available for 1XY7)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1XY7)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1XY7)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1XY7)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1XY7)

(-) Exons   (0, 0)

(no "Exon" information available for 1XY7)

(-) 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:120
 aligned with Y5848_ARATH | Q9LV66 from UniProtKB/Swiss-Prot  Length:166

    Alignment length:135
                                    29        39        49        59        69        79        89        99       109       119       129       139       149     
          Y5848_ARATH    20 HLVFTEFKQMLLVEAQKVGDAVTFYKSAFGAIESGHSLYPKRKLDQELPHVLSSELNLAGSSFVVCDVSSLPGFSTAKSEGSGVTFLLGTKDAEAAVAKAVDAGAVKVEVTEAEVELGFKGKVTDPFGVTWIFAE 154
               SCOP domains d1xy7a_ A: Hypothetical protein At               5g48480                                                                                SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeeeeee...hhhhhhhhhhhhhh.ee.---------------...eeeeee..eeeeeee.hhh.............eeeee..hhhhhhhhhhhh..ee...hhhhhhh.eeeeee.....eeeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1xy7 A  20 HLVFTEFKQmLLVEAQKVGDAVTFYKSAFGAIES---------------HVLSSELNLAGSSFVVCDVSSLPGFSTAKSEGSGVTFLLGTKDAEAAVAKAVDAGAVKVEVTEAEVELGFKGKVTDPFGVTWIFAE 154
                                    29        39        49   |     -        69        79        89        99       109       119       129       139       149     
                                    29-MSE                  53              69                                                                                     


Chain B from PDB  Type:PROTEIN  Length:122
 aligned with Y5848_ARATH | Q9LV66 from UniProtKB/Swiss-Prot  Length:166

    Alignment length:133
                                    31        41        51        61        71        81        91       101       111       121       131       141       151   
          Y5848_ARATH    22 VFTEFKQMLLVEAQKVGDAVTFYKSAFGAIESGHSLYPKRKLDQELPHVLSSELNLAGSSFVVCDVSSLPGFSTAKSEGSGVTFLLGTKDAEAAVAKAVDAGAVKVEVTEAEVELGFKGKVTDPFGVTWIFAE 154
               SCOP domains d1xy7b_ B: Hypothetical protein At5g           48480                                                                                  SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeeee...hhhhhhhhhhhhhh.eeeeee.-----------...eeeeee..eeeeeee.hhh.............eeeee..hhhhhhhhhhhh..ee...hhhhhhh.eeeeee.....eeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1xy7 B  22 VFTEFKQmLLVEAQKVGDAVTFYKSAFGAIESGHSL-----------HVLSSELNLAGSSFVVCDVSSLPGFSTAKSEGSGVTFLLGTKDAEAAVAKAVDAGAVKVEVTEAEVELGFKGKVTDPFGVTWIFAE 154
                                   |31        41        51     |   -       |71        81        91       101       111       121       131       141       151   
                                  29-MSE                      57          69
   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/Biological Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 1XY7)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1XY7)

(-) Gene Ontology  (2, 2)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (Y5848_ARATH | Q9LV66)
biological process
    GO:0008150    biological_process    Any process specifically pertinent to the functioning of integrated living units: cells, tissues, organs, and organisms. A process is a collection of molecular events with a defined beginning and end.
cellular component
    GO:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.

 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
    MSE  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
(no "Sites" information available for 1xy7)
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 1xy7)
 

(-) 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 ](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
  1xy7
    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
  Y5848_ARATH | Q9LV66
    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
  Y5848_ARATH | Q9LV66
    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
        Y5848_ARATH | Q9LV66: 2q48

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 1XY7)