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

(-) Description

Title :  CRYSTAL STRUCTURE OF GAMMA-B CRYSTALLIN EXPRESSED IN E. COLI BASED ON MRNA VARIANT 2
 
Authors :  D. Kudlinzki, F. Buhr, V. L. Linhard, S. Jha, A. A. Komar, H. Schwalbe
Date :  27 Aug 14  (Deposition) - 09 Sep 15  (Release) - 09 Sep 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.38
Chains :  Asym./Biol. Unit :  A
Keywords :  Eye Lens Protein, Structural Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  F. Buhr, S. Jha, M. Thommen, M. Rodnina, F. Kutz, D. Kudlinzki, V. L. Linhard, A. A. Komar, H. Schwalbe
Two Synonymous Gene Variants Encode Proteins With Identical Sequence, But Different Folding Conformations.
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - GAMMA-CRYSTALLIN B
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Taxid: 469008
    Gene: CRYGB
    Organism Common: BOVINE
    Organism Scientific: BOS TAURUS
    Organism Taxid: 9913
    Synonym: GAMMA-B-CRYSTALLIN,GAMMA-CRYSTALLIN II

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 4W9A)

(-) Sites  (0, 0)

(no "Site" information available for 4W9A)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4W9A)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4W9A)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4W9A)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4W9A)

(-) Exons   (0, 0)

(no "Exon" information available for 4W9A)

(-) 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:172
                                                                                                                                                                                                            
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeehhheeeeeee...............eeeeee..eeeeeehhheeeeeee..eee.hhhhhh.......eeee........eeeeeeehhheeeeeee.....hhhhhhh.....eeeeee..eeeeee...eeeeeee..eee.hhhhhh.......eeee... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4w9a A   2 GKITFYEDRGFQGHCYECSSDCPNLQPYFSRCNSIRVDSGCWMLYERPNYQGHQYFLRRGDYPDYQQWMGFNDSIRSCRLIPQHTGTFRMRIYERDDFRGQMSEITDDCPSLQDRFHLTEVHSLNVLEGSWVLYEMPSYRGRQYLLRPGEYRRYLDWGAMNAKVGSLRRVMD 173
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171
   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 4W9A)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4W9A)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4W9A)

(-) Gene Ontology  (7, 7)

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
(no "Ligands, Modified Residues, Ions" information available for 4w9a)
 
  Sites
(no "Sites" information available for 4w9a)
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 4w9a)
 

(-) 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
  4w9a
    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
  CRGB_BOVIN | P02526
    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
  CRGB_BOVIN | P02526
    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
        CRGB_BOVIN | P02526: 1amm 1dsl 1gam 1gcs 1i5i 4gcr 4w9b

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 4W9A)