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 :  CRYSTAL STRUCTURE OF 2-FLUOROHISTINE LABELED PROTECTIVE ANTIGEN (PH 5.8)
 
Authors :  S. Lovell, K. P. Battaile, M. Rajapaksha, B. E. Janowiak, K. K. Andra, J.
Date :  06 Jan 11  (Deposition) - 15 Feb 12  (Release) - 03 Oct 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.10
Chains :  Asym./Biol. Unit :  A
Keywords :  Protective Antigen; 2-Fluorohistidine; Anthrax; Ph Stability, Protein Binding (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  M. Rajapaksha, S. Lovell, B. E. Janowiak, K. K. Andra, K. P. Battaile, J. G. Bann
Ph Effects On Binding Between The Anthrax Protective Antige And The Host Cellular Receptor Cmg2.
Protein Sci. V. 21 1467 2012
PubMed-ID: 22855243  |  Reference-DOI: 10.1002/PRO.2136

(-) Compounds

Molecule 1 - PROTECTIVE ANTIGEN
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPQE80
    Expression System StrainUTH780
    Expression System Taxid562
    Expression System Vector TypePLASMID
    GenePAGA, PAG, PXO1-110, BXA0164, GBAA_PXO1_0164
    Organism CommonANTHRAX,ANTHRAX BACTERIUM
    Organism ScientificBACILLUS ANTHRACIS
    Organism Taxid1392
    SynonymPA, ANTHRAX TOXINS TRANSLOCATING PROTEIN, PA-83, PA83, PROTECTIVE ANTIGEN PA-20, PA20, PROTECTIVE ANTIGEN PA-63, PA63

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 11)

Asymmetric/Biological Unit (3, 11)
No.NameCountTypeFull Name
12HF7Mod. Amino Acid2-FLUORO-L-HISTIDINE
2CA2Ligand/IonCALCIUM ION
3PG42Ligand/IonTETRAETHYLENE GLYCOL

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:179 , ASP A:181 , GLU A:188 , SER A:222 , LYS A:225 , ASP A:235BINDING SITE FOR RESIDUE CA A 736
2AC2SOFTWAREASP A:177 , ASP A:179 , ASP A:181 , ILE A:183 , GLU A:188 , HOH A:750BINDING SITE FOR RESIDUE CA A 737
3AC3SOFTWARESER A:294 , SER A:296 , THR A:331 , LYS A:703BINDING SITE FOR RESIDUE PG4 A 738
4AC4SOFTWAREASN A:408 , TYR A:410 , LYS A:496BINDING SITE FOR RESIDUE PG4 A 739

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3Q8F)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Tyr A:411 -Pro A:412

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (5, 5)

Asymmetric/Biological Unit (5, 5)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_PAG_BACAN_001 *M295IPAG_BACAN  ---  ---AM266I
2UniProtVAR_PAG_BACAN_002 *N392DPAG_BACAN  ---  ---AN363D
3UniProtVAR_PAG_BACAN_003 *F560LPAG_BACAN  ---  ---AF531L
4UniProtVAR_PAG_BACAN_004 *P565SPAG_BACAN  ---  ---AP536S
5UniProtVAR_PAG_BACAN_005 *A600VPAG_BACAN  ---  ---AA571V
   * ID not provided by source

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3Q8F)

(-) Exons   (0, 0)

(no "Exon" information available for 3Q8F)

(-) 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:645
 aligned with PAG_BACAN | P13423 from UniProtKB/Swiss-Prot  Length:764

    Alignment length:719
                                    54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404       414       424       434       444       454       464       474       484       494       504       514       524       534       544       554       564       574       584       594       604       614       624       634       644       654       664       674       684       694       704       714       724       734       744       754         
            PAG_BACAN    45 SQGLLGYYFSDLNFQAPMVVTSSTTGDLSIPSSELENIPSENQYFQSAIWSGFIKVKKSDEYTFATSADNHVTMWVDDQEVINKASNSNKIRLEKGRLYQIKIQYQRENPTEKGLDFKLYWTDSQNKKEVISSDNLQLPELKQKSSNSRKKRSTSAGPTVPDRDNDGIPDSLEVEGYTVDVKNKRTFLSPWISNIHEKKGLTKYKSSPEKWSTASDPYSDFEKVTGRIDKNVSPEARHPLVAAYPIVHVDMENIILSKNEDQSTQNTDSQTRTISKNTSTSRTHTSEVHGNAEVHASFFDIGGSVSAGFSNSNSSTVAIDHSLSLAGERTWAETMGLNTADTARLNANIRYVNTGTAPIYNVLPTTSLVLGKNQTLATIKAKENQLSQILAPNNYYPSKNLAPIALNAQDDFSSTPITMNYNQFLELEKTKQLRLDTDQVYGNIATYNFENGRVRVDTGSNWSEVLPQIQETTARIIFNGKDLNLVERRIAAVNPSDPLETTKPDMTLKEALKIAFGFNEPNGNLQYQGKDITEFDFNFDQQTSQNIKNQLAELNATNIYTVLDKIKLNAKMNILIRDKRFHYDRNNIAVGADESVVKEAHREVINSSTEGLLLNIDKDIRKILSGYIVEIEDTEGLKEVINDRYDMLNISSLRQDGKTFIDFKKYNDKLPLYISNPNYKVNVYAVTKENTIINPSENGDTSTNGIKKILIFSKKGYEI 763
               SCOP domains d3q8fa2 A:16-225 PA14                                                                                                                                                                                             d3q8fa1 A:226-734 Anthrax protective antigen C-te            rminal-like                                                                                                                                                                                                                                                                                                                                                                                                                                                      SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeee.......eeeeeee.......hhhhh----.......eeeeeeee..--.eee.--......eeeee...eee.-----..eee.....eeeeeeee.............eee.....eee.....ee......--------------...........hhhhhhhheeeee..-.eeeee.---------..................hhhhhhhh......hhhhhh........eeeeeeeeeeee.------------.eeeeeeeeee...---------------------......eeeeeee.......---hhhhhh......eeeeeeeeeeee............eeeee...eeeeee..............eee.......ee....-.......eeehhhhhhhhhhheeeeee.....eeeeee....eeeeeeeeehhhhhhhhhhheeeeee.......eeeeee.....hhhhh....eehhhhhhhhhh........ee..ee...eeeeehhhhhhhhhhhhhhh...hhhhhhhh.ee....eeeeee..eee.....eeeehhhhhhhh...eeeee..eeee..hhhhhhheeeeeeeee.....eee..........eee.....eeee.................eeeeeeee.hhh.................eeeeeee.hhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------I------------------------------------------------------------------------------------------------D-----------------------------------------------------------------------------------------------------------------------------------------------------------------------L----S----------------------------------V------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3q8f A  16 SQGLLGYYFSDLNFQAPMVVTSSTTGDLSIPSSEL----SENQYFQSAIWSGFIKV--SDEYT--TSADNhVTMWVDDQEVIN-----NKIRLEKGRLYQIKIQYQRENPTEKGLDFKLYWTDSQNKKEVISSDNLQLPELKQ--------------PTVPDRDNDGIPDSLEVEGYTVDVKN-RTFLSPW---------LTKYKSSPEKWSTASDPYSDFEKVTGRIDKNVSPEARhPLVAAYPIVhVDMENIILSKN------------RTISKNTSTSRThT---------------------AGFSNSNSSTVAIDhSLSLA---TWAETMGLNTADTARLNANIRYVNTGTAPIYNVLPTTSLVLGKNQTLATIKAKENQLSQILAPNNYYPSKNLAPIALNAQ-DFSSTPITMNYNQFLELEKTKQLRLDTDQVYGNIATYNFENGRVRVDTGSNWSEVLPQIQETTARIIFNGKDLNLVERRIAAVNPSDPLETTKPDMTLKEALKIAFGFNEPNGNLQYQGKDITEFDFNFDQQTSQNIKNQLAELNATNIYTVLDKIKLNAKMNILIRDKRFhYDRNNIAVGADESVVKEAhREVINSSTEGLLLNIDKDIRKILSGYIVEIEDTEGLKEVINDRYDMLNISSLRQDGKTFIDFKKYNDKLPLYISNPNYKVNVYAVTKENTIINPSENGDTSTNGIKKILIFSKKGYEI 734
                                    25        35        45    |   55        65     |  75  |  |  85|       95  |    105       115       125       135       145       155  |      -       175       185       195  | |  205|        -|      225       235       245       255       265        |-         - |     295   ||    -         -      |325       335|    | 345       355       365       375       385       395       405       415        |-|      435       445       455       465       475       485       495       505       515       525       535       545       555       565       575       585       595 |     605       615|      625       635       645       655       665       675       685       695       705       715       725         
                                                             50   55              71 74  78 81    |          98   104                                                   158            173                      198 |   206       216                                  253-2HF   263-2HF    274          287         299-2HF                322           336-2HF1 345                                                                            424 |                                                                                                                                                                        597-2HF            616-2HF                                                                                                                  
                                                                                                 86-2HF                                                                                                           200                                                                                                 300                                                                                                                           426                                                                                                                                                                                                                                                                                                                    

   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  (2, 2)

Asymmetric/Biological Unit

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3Q8F)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3Q8F)

(-) Gene Ontology  (18, 18)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (PAG_BACAN | P13423)
molecular function
    GO:0042802    identical protein binding    Interacting selectively and non-covalently with an identical protein or proteins.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
biological process
    GO:0043409    negative regulation of MAPK cascade    Any process that stops, prevents, or reduces the frequency, rate or extent of signal transduction mediated by the MAPKKK cascade.
    GO:0010629    negative regulation of gene expression    Any process that decreases the frequency, rate or extent of gene expression. Gene expression is the process in which a gene's coding sequence is converted into a mature gene product or products (proteins or RNA). This includes the production of an RNA transcript as well as any processing to produce a mature RNA product or an mRNA or circRNA (for protein-coding genes) and the translation of that mRNA or circRNA into protein. Protein maturation is included when required to form an active form of a product from an inactive precursor form.
    GO:0001933    negative regulation of protein phosphorylation    Any process that stops, prevents or reduces the rate of addition of phosphate groups to amino acids within a protein.
    GO:0000122    negative regulation of transcription from RNA polymerase II promoter    Any process that stops, prevents, or reduces the frequency, rate or extent of transcription from an RNA polymerase II promoter.
    GO:0009405    pathogenesis    The set of specific processes that generate the ability of an organism to induce an abnormal, generally detrimental state in another organism.
    GO:0044533    positive regulation of apoptotic process in other organism    Any process in which an organism activates, maintains or increases the frequency, rate or extent of programmed cell death by apoptosis in a second organism.
    GO:0097300    programmed necrotic cell death    A necrotic cell death process that results from the activation of endogenous cellular processes, such as signaling involving death domain receptors or Toll-like receptors.
    GO:0051260    protein homooligomerization    The process of creating protein oligomers, compounds composed of a small number, usually between three and ten, of identical component monomers. Oligomers may be formed by the polymerization of a number of monomers or the depolymerization of a large protein polymer.
    GO:0035897    proteolysis in other organism    The chemical reactions and pathways performed by an organism resulting in the hydrolysis of proteins in another organism by cleavage of their peptide bonds.
    GO:1903140    regulation of establishment of endothelial barrier    Any process that modulates the frequency, rate or extent of establishment of endothelial barrier.
    GO:0061136    regulation of proteasomal protein catabolic process    Any process that modulates the rate, frequency, or extent of the chemical reactions and pathways resulting in the breakdown of a protein or peptide by hydrolysis of its peptide bonds that is mediated by the proteasome.
cellular component
    GO:0010008    endosome membrane    The lipid bilayer surrounding an endosome.
    GO:0005576    extracellular region    The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.
    GO:0005615    extracellular space    That part of a multicellular organism outside the cells proper, usually taken to be outside the plasma membranes, and occupied by fluid.
    GO:0005886    plasma membrane    The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.

 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
    2HF  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    CA  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    PG4  [ 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
    Tyr A:411 - Pro A:412   [ RasMol ]  
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  3q8f
    Family and Domain InformationProDom | SYSTERS
    General Structural InformationGlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in MembranesOPM
    Protein SurfaceSURFACE
    Secondary StructureDSSP (structure derived) | HSSP (homology derived)
    Structural GenomicsGeneCensus
    Structural NeighboursCE | VAST
    Structure ClassificationCATH | Dali | SCOP
    Validation and Original DataBMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  PAG_BACAN | P13423
    Comparative Protein Structure ModelsModBase
    Genomic InformationEnsembl
    Protein-protein InteractionDIP
    Sequence, Family and Domain InformationInterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  (no 'Enzyme Classificator' available)
    General Enzyme InformationBRENDA | EC-PDB | Enzyme | IntEnz
    PathwayKEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease InformationOMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related InformationGenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain InformationXDom
    Interatomic Contacts of Structural UnitsCSU
    Ligand-protein ContactsLPC
    Protein CavitiescastP
    Sequence and Secondary StructurePDBCartoon
    Structure AlignmentSTRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence BrowserSTING
 
Access by UniProt ID/Accession number
  PAG_BACAN | P13423
    Protein Disorder PredictionDisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        PAG_BACAN | P134231acc 1t6b 1tx5 1tzn 1tzo 1v36 3etb 3ino 3j9c 3kwv 3mhz 3q8a 3q8b 3q8c 3q8e 3tew 3tex 3tey 3tez 4ee2 4h2a 4nam 5fr3

(-) Related Entries Specified in the PDB File

3q8a 3q8b 3q8c 3q8e