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 :  STRUCTURE OF THE UNIVERSAL STRESS PROTEIN FROM ARCHAEOGLOBUS FULGIDUS IN COMPLEX WITH DAMP
 
Authors :  K. L. Tkaczuk, I. A. Shumilin, M. Chruszcz, M. Cymborowski, X. Xu, R. Di A. Savchenko, A. Joachimiak, W. Minor, Midwest Center For Structu Genomics (Mcsg)
Date :  22 Feb 11  (Deposition) - 30 Mar 11  (Release) - 26 Jun 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.10
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Structural Genomics, Psi-Biology, Midwest Center For Structural Genomics, Mcsg, A/B Class, Rfm Like, Putative Universal Stress Protein, Unknown Function (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  K. L. Tkaczuk, I. A. Shumilin, M. Chruszcz, E. Evdokimova, A. Savchenko, W. Minor
Structural And Functional Insight Into The Universal Stress Protein Family.
Evol Appl V. 6 434 2013
PubMed-ID: 23745136  |  Reference-DOI: 10.1111/EVA.12057

(-) Compounds

Molecule 1 - UNCHARACTERIZED PROTEIN
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: P15TV LIC
    Expression System Strain: BL21-CODONPLUS(DE3)-RIPL
    Expression System Taxid: 511693
    Expression System Vector Type: PLASMID
    Gene: AF_0826
    Organism Scientific: ARCHAEOGLOBUS FULGIDUS
    Organism Taxid: 2234

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 7)

Asymmetric/Biological Unit (3, 7)
No.NameCountTypeFull Name
1ACT3Ligand/IonACETATE ION
2D5M1Ligand/Ion2'-DEOXYADENOSINE-5'-MONOPHOSPHATE
3MSE3Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREALA A:9 , VAL A:10 , ASP A:11 , HIS A:39 , SER A:40 , PRO A:84 , GLY A:103 , GLY A:116 , SER A:117 , VAL A:118 , ALA A:119 , HOH A:164BINDING SITE FOR RESIDUE D5M A 135
2AC2SOFTWARELYS A:13 , ARG B:80BINDING SITE FOR RESIDUE ACT B 135
3AC3SOFTWAREASP B:11 , LYS B:12 , ARG B:16 , ARG B:107BINDING SITE FOR RESIDUE ACT B 136
4AC4SOFTWAREGLY B:44 , THR B:110 , LYS B:112BINDING SITE FOR RESIDUE ACT B 137

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3QTB)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3QTB)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3QTB)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3QTB)

(-) Exons   (0, 0)

(no "Exon" information available for 3QTB)

(-) 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:125
 aligned with O29432_ARCFU | O29432 from UniProtKB/TrEMBL  Length:134

    Alignment length:134
                                    10        20        30        40        50        60        70        80        90       100       110       120       130    
         O29432_ARCFU     1 MIYMPIVVAVDKKSDRAERVLRFAAEEARLRGVPVYVVHSLPGGGRTKDEDIIEAKETLSWAVSIIRKEGAEGEEHLLVRGKEPPDDIVDFADEVDAIAIVIGIRKRSPTGKLIFGSVARDVILKANKPVICIK 134
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeee....hhhhhhhhhhhhhhhhhhh..eeeeeee.hhhhhhhhhhhhhhhhhhhhhhhhhhh...eeeeeee...hhhhhhhhhhhhh...eeeee..---------.hhhhhhhhhhh...eeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3qtb A   1 mIYmPIVVAVDKKSDRAERVLRFAAEEARLRGVPVYVVHSLPGGGRTKDEDIIEAKETLSWAVSIIRKEGAEGEEHLLVRGKEPPDDIVDFADEVDAIAIVIGIR---------FGSVARDVILKANKPVICIK 134
                            |  |    10        20        30        40        50        60        70        80        90       100    |    -    |  120       130    
                            |  |                                                                                                  105       115                   
                            1-MSE                                                                                                                                 
                               4-MSE                                                                                                                              


Chain B from PDB  Type:PROTEIN  Length:133
 aligned with O29432_ARCFU | O29432 from UniProtKB/TrEMBL  Length:134

    Alignment length:133
                                    11        21        31        41        51        61        71        81        91       101       111       121       131   
         O29432_ARCFU     2 IYMPIVVAVDKKSDRAERVLRFAAEEARLRGVPVYVVHSLPGGGRTKDEDIIEAKETLSWAVSIIRKEGAEGEEHLLVRGKEPPDDIVDFADEVDAIAIVIGIRKRSPTGKLIFGSVARDVILKANKPVICIK 134
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) Usp-3qtbB01 B:2-134                                                                                                                   Pfam domains (1)
           Pfam domains (2) Usp-3qtbB02 B:2-134                                                                                                                   Pfam domains (2)
         Sec.struct. author ....eeee....hhhhhhhhhhhhhhhhhhh..eeeeeee.hhhhhhhhhhhhhhhhhhhhhhhhhhh...eeeeeee...hhhhhhhhhhhhhh..eeeee.eee.....eeehhhhhhhhhhh...eeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3qtb B   2 IYmPIVVAVDKKSDRAERVLRFAAEEARLRGVPVYVVHSLPGGGRTKDEDIIEAKETLSWAVSIIRKEGAEGEEHLLVRGKEPPDDIVDFADEVDAIAIVIGIRKRSPTGKLIFGSVARDVILKANKPVICIK 134
                              |     11        21        31        41        51        61        71        81        91       101       111       121       131   
                              4-MSE
   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 3QTB)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3QTB)

(-) Pfam Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Clan: HUP (230)

(-) Gene Ontology  (1, 1)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (O29432_ARCFU | O29432)
biological process
    GO:0006950    response to stress    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a disturbance in organismal or cellular homeostasis, usually, but not necessarily, exogenous (e.g. temperature, humidity, ionizing radiation).

 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 ]
    D5M  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    MSE  [ 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
(no "Cis Peptide Bonds" information available for 3qtb)
 

(-) 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
  3qtb
    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
  O29432_ARCFU | O29432
    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)
  (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
  O29432_ARCFU | O29432
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/TrEMBL
        O29432_ARCFU | O29432: 3dlo

(-) Related Entries Specified in the PDB File

3dlo RELATED ID: APC7551 RELATED DB: TARGETDB