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 :  CRYSTALLOGRAPHIC STRUCTURE OF THIOREDOXIN FROM LITOPENAEUS VANNAMEI: RADIATION DAMAGE EFFECT AT 3.4 MGY, FOCUSED IN DISULFIDE BONDS.
 
Authors :  A. A. Campos-Acevedo, E. Rudino-Pinera
Date :  10 Oct 14  (Deposition) - 14 Jan 15  (Release) - 14 Jan 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.65
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Oxidoreductase, Thioredoxin, Shrimp, Litopenaeus Vannamie, Radiation Damage, Disulfide Bond (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. A. Campos-Acevedo, E. Rudino-Pinera
Crystallographic Studies Evidencing The High Energy Tolerance To Disrupting The Interface Disulfide Bond Of Thioredoxin 1 From White Leg Shrimp Litopenaeus Vannamei.
Molecules V. 19 21113 2014
PubMed-ID: 25517346  |  Reference-DOI: 10.3390/MOLECULES191221113

(-) Compounds

Molecule 1 - THIOREDOXIN
    Chains: A, B
    EC Number: 1.8.1.9
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET11A
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Mutation: YES
    Organism Common: PACIFIC WHITE SHRIMP
    Organism Scientific: LITOPENAEUS VANNAMEI
    Organism Taxid: 6689
    Other Details: RESIDUE 11 IS SER IN UNIPROT DEPOSIT B1PWB9, IN THIS STRUCTURE A PHE IS CLEARLY VISIBLE ON POSITION 11.

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 4)

Asymmetric/Biological Unit (3, 4)
No.NameCountTypeFull Name
1ACT1Ligand/IonACETATE ION
2GOL2Ligand/IonGLYCEROL
3SO41Ligand/IonSULFATE ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:7 , GLN A:8 , GLU A:9 , HOH A:2024 , MET B:49 , ASP B:51 , LYS B:105 , HOH B:2090BINDING SITE FOR RESIDUE SO4 B1106
2AC2SOFTWARELYS B:13 , GLU B:17 , ALA B:18 , ASN B:20 , LYS B:21 , HOH B:2030BINDING SITE FOR RESIDUE ACT B1107
3AC3SOFTWARETHR A:12 , LEU A:15 , ASN A:16 , ASN A:82 , GLY A:83 , HOH A:2035 , HOH A:2085 , LYS B:41 , GLU B:44 , HOH B:2051 , HOH B:2052BINDING SITE FOR RESIDUE GOL A1106
4AC4SOFTWAREGLU A:17 , ALA A:18 , LYS A:21 , VAL A:53 , HOH A:2103BINDING SITE FOR RESIDUE GOL A1107

(-) SS Bonds  (3, 3)

Asymmetric/Biological Unit
No.Residues
1A:32 -A:35
2A:73 -B:73
3B:32 -B:35

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Met A:74 -Pro A:75
2Met B:74 -Pro B:75

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4V2L)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4V2L)

(-) Exons   (0, 0)

(no "Exon" information available for 4V2L)

(-) 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:105
                                                                                                                                         
               SCOP domains --------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..ee..hhhhhhhhhhhh...eeeeeee...hhhhhhhhhhhhhhhhhh..eeeeeee...hhhhhhhh......eeeeee..eeeeeee..hhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------- Transcript
                 4v2l A   1 MVYQVKDQEDFTKQLNEAGNKLVVIDFYATWCGPCKMIAPKLEELSQSMSDVVFLKVDVDECEDIAQDNQIACMPTFLFMKNGQKLDSLSGANYDKLLELVEKNK 105
                                    10        20        30        40        50        60        70        80        90       100     


Chain B from PDB  Type:PROTEIN  Length:105
                                                                                                                                         
               SCOP domains --------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eee..hhhhhhhhhhhh...eeeeeee...hhhhhhhhhhhhhhhhhh..eeeeeee...hhhhhhhh......eeeeee..eeeeeee..hhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------- Transcript
                 4v2l B   1 MVYQVKDQEDFTKQLNEAGNKLVVIDFYATWCGPCKMIAPKLEELSQSMSDVVFLKVDVDECEDIAQDNQIACMPTFLFMKNGQKLDSLSGANYDKLLELVEKNK 105
                                    10        20        30        40        50        60        70        80        90       100
   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 4V2L)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4V2L)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4V2L)

(-) Gene Ontology  (5, 5)

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
    ACT  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    GOL  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    SO4  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
    AC4  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Met A:74 - Pro A:75   [ RasMol ]  
    Met B:74 - Pro B:75   [ RasMol ]  
 

(-) 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
  4v2l
    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
  B1PWB9_LITVA | B1PWB9
    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)
  1.8.1.9
    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
  B1PWB9_LITVA | B1PWB9
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/TrEMBL
        B1PWB9_LITVA | B1PWB9: 3zzx 4aj6 4aj7 4aj8 4v2m 4v2n 5g2z 5g30 5g31

(-) Related Entries Specified in the PDB File

4v2m CRYSTALLOGRAPHIC STRUCTURE OF THIOREDOXIN FROM LITOPENAEUS VANNAMEI: RADIATION DAMAGE EFFECT AT 34 MGY, FOCUSED IN DISULFIDE BONDS.
4v2n CRYSTALLOGRAPHIC STRUCTURE OF THIOREDOXIN FROM LITOPENAEUS VANNAMEI: RADIATION DAMAGE EFFECT AT 85 MGY, FOCUSED IN DISULFIDE BONDS