Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asymmetric Unit
(-)Asym. Unit - sites
(-)Biological Unit 1
(-)Biol. Unit 1 - sites
(-)Biological Unit 2
collapse expand < >
Image Asymmetric Unit
Asymmetric Unit  (Jmol Viewer)
Image Asym. Unit - sites
Asym. Unit - sites  (Jmol Viewer)
Image Biological Unit 1
Biological Unit 1  (Jmol Viewer)
Image Biol. Unit 1 - sites
Biol. Unit 1 - sites  (Jmol Viewer)
Image Biological Unit 2
Biological Unit 2  (Jmol Viewer)

(-) Description

Title :  CRYSTAL STRUCTURE OF ANCESTRAL THIOREDOXIN RELATIVE TO LAST EUKARYOTES COMMON ANCESTOR (LECA) FROM THE PRECAMBRIAN PERIOD
 
Authors :  J. A. Gavira, A. Ingles-Prieto, B. Ibarra-Molero, J. M. Sanchez-Ruiz
Date :  24 Oct 12  (Deposition) - 21 Aug 13  (Release) - 25 Sep 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.30
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Oxidoreductase, Ancestral Reconstructed (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. Ingles-Prieto, B. Ibarra-Molero, A. Delgado-Delgado, R. Perez-Jimenez, J. M. Fernandez, E. A. Gaucher, J. M. Sanchez-Ruiz, J. A. Gavira
Conservation Of Protein Structure Over Four Billion Years
Structure V. 21 1690 2013
PubMed-ID: 23932589  |  Reference-DOI: 10.1016/J.STR.2013.06.020

(-) Compounds

Molecule 1 - LECA THIOREDOXIN
    Chains: A, B
    EC Number: 1.8.1.9
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET30A PLUS
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Organism Scientific: SYNTHETIC CONSTRUCT
    Organism Taxid: 32630
    Other Details: ANCESTRAL, RECONSTRUCTED PHYLOGENETICALLY

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): A 
Biological Unit 2 (1x):  B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 7)

Asymmetric Unit (4, 7)
No.NameCountTypeFull Name
1ACT1Ligand/IonACETATE ION
2CL1Ligand/IonCHLORIDE ION
3MG2Ligand/IonMAGNESIUM ION
4NA3Ligand/IonSODIUM ION
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1ACT1Ligand/IonACETATE ION
2CL-1Ligand/IonCHLORIDE ION
3MG-1Ligand/IonMAGNESIUM ION
4NA-1Ligand/IonSODIUM ION
Biological Unit 2 (0, 0)
No.NameCountTypeFull Name
1ACT-1Ligand/IonACETATE ION
2CL-1Ligand/IonCHLORIDE ION
3MG-1Ligand/IonMAGNESIUM ION
4NA-1Ligand/IonSODIUM ION

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELYS A:81 , HIS A:104BINDING SITE FOR RESIDUE CL A1107
2AC2SOFTWAREMET A:1 , HOH A:2051 , HOH A:2064 , HOH A:2220BINDING SITE FOR RESIDUE NA A1108
3AC3SOFTWAREMET A:1 , PHE A:54 , HOH A:2124 , HOH A:2221BINDING SITE FOR RESIDUE NA A1109
4AC4SOFTWARETHR A:29 , HOH A:2137 , HOH A:2143 , HOH A:2222BINDING SITE FOR RESIDUE MG A1110
5AC5SOFTWARETHR A:6 , ASN A:7 , LYS A:8 , GLU A:61 , VAL A:62 , ASP A:64 , ASN A:82 , HOH A:2019 , HOH A:2028 , HOH A:2144 , HOH A:2223BINDING SITE FOR RESIDUE ACT A1111
6AC6SOFTWAREHOH A:2040 , HOH A:2058 , HOH A:2060 , HOH A:2116 , HOH A:2224 , HOH A:2225BINDING SITE FOR RESIDUE MG A1112
7AC7SOFTWAREPRO B:106 , HOH B:2193 , HOH B:2198 , HOH B:2199BINDING SITE FOR RESIDUE NA B1107

(-) SS Bonds  (2, 2)

Asymmetric Unit
No.Residues
1A:31 -A:34
2B:31 -B:34

(-) Cis Peptide Bonds  (2, 2)

Asymmetric 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 2YOI)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2YOI)

(-) Exons   (0, 0)

(no "Exon" information available for 2YOI)

(-) 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:106
                                                                                                                                          
               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
                 2yoi A   1 MVIQVTNKEEFEAILSEADKLVVVDFFATWCGPCKMIAPFFEELSEEYPDKVVFIKVDVDEVPDVAAKYGITSMPTFKFFKNGKKVDELVGANQEKLKQMILKHAP 106
                                    10        20        30        40        50        60        70        80        90       100      


Chain B from PDB  Type:PROTEIN  Length:106
                                                                                                                                          
               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
                 2yoi B   1 MVIQVTNKEEFEAILSEADKLVVVDFFATWCGPCKMIAPFFEELSEEYPDKVVFIKVDVDEVPDVAAKYGITSMPTFKFFKNGKKVDELVGANQEKLKQMILKHAP 106
                                    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 2YOI)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2YOI)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2YOI)

(-) Gene Ontology  (0, 0)

Asymmetric Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 2YOI)

 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
    ACT  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    CL  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    MG  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    NA  [ 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 ]
 
  Cis Peptide Bonds
    Met A:74 - Pro A:75   [ RasMol ]  
    Met B:74 - Pro B:75   [ RasMol ]  
 
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
[ Asym. Unit PNG format | Asym. Unit - sites PNG format | Biol. Unit 1 PNG format | Biol. Unit 1 - sites PNG format | Biol. Unit 2 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
  2yoi
    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
  (no 'UniProt ID/Accession number' available) |
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProt
 
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
  (no 'UniProt ID/Accession number' available) |
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT

 Related Entries

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

(no "Entries Sharing at Least One Protein Chain" available for 2YOI)

(-) Related Entries Specified in the PDB File

2yj7 CRYSTAL STRUCTURE OF A HYPERSTABLE PROTEIN FROM THE PRECAMBRIAN PERIOD
2yn1 CRYSTAL STRUCTURE OF ANCESTRAL THIOREDOXIN RELATIVE TO LAST GAMMA-PROTEOBACTERIA COMMON ANCESTOR (LGPCA) FROM THE PRECAMBRIAN PERIOD
2ynx CRYSTAL STRUCTURE OF ANCESTRAL THIOREDOXIN RELATIVE TO LAST ARCHAEA COMMON ANCESTOR (LACA) FROM THE PRECAMBRIAN PERIOD
2ypm CRYSTAL STRUCTURE OF ANCESTRAL THIOREDOXIN RELATIVE TO LAST ANIMAL AND FUNGI COMMON ANCESTOR (LAFCA) FROM THE PRECAMBRIAN PERIOD
3ziv CRYSTAL STRUCTURE OF ANCESTRAL THIOREDOXIN RELATIVE TO LAST ARCHAEA-EUKARYOTES COMMON ANCESTOR (AECA) FROM THE PRECAMBRIAN PERIOD
4ba7 CRYSTAL STRUCTURE OF ANCESTRAL THIOREDOXIN RELATIVE TO LAST BACTERIA COMMON ANCESTOR (LBCA) FROM THE PRECAMBRIAN PERIOD