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 TREPONEMA PALLIDUM TP0796 FLAVIN TRAFFICKING PROTEIN, A BIFUNCTIONAL FMN TRANSFERASE/FAD PYROPHOSPHATASE, D284A MUTANT, ADN BOUND FORM
 
Authors :  D. R. Tomchick, C. A. Brautigam, R. K. Deka, M. V. Norgard
Date :  19 Dec 14  (Deposition) - 14 Oct 15  (Release) - 14 Oct 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.40
Chains :  Asym./Biol. Unit :  A
Keywords :  Fmn Transferase, Fad Pyrophosphatase, Hydrolase, Bimetal Center, Flavin Turnover, Treponema Pallidum, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  R. K. Deka, C. A. Brautigam, W. Z. Liu, D. R. Tomchick, M. V. Norgard
Evidence For Posttranslational Protein Flavinylation In The Syphilis Spirochete Treponema Pallidum: Structural And Biochemical Insights From The Catalytic Core Of A Periplasmic Flavin-Trafficking Protein.
Mbio V. 6 00519 2015
PubMed-ID: 25944861  |  Reference-DOI: 10.1128/MBIO.00519-15

(-) Compounds

Molecule 1
    Chains: A
    EC Number: 2.7.1.180
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: APBE, TP_0796
    Mutation: YES
    Organism Scientific: TREPONEMA PALLIDUM (STRAIN NICHOLS)
    Organism Taxid: 243276
    Strain: NICHOLS
    Synonym: FLAVIN TRANSFERASE

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 13)

Asymmetric/Biological Unit (4, 13)
No.NameCountTypeFull Name
1ACT6Ligand/IonACETATE ION
2ADN1Ligand/IonADENOSINE
3EDO5Ligand/Ion1,2-ETHANEDIOL
4MG1Ligand/IonMAGNESIUM ION

(-) Sites  (13, 13)

Asymmetric Unit (13, 13)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREHIS A:267 , HOH A:628 , HOH A:671 , HOH A:675 , HOH A:694binding site for residue MG A 401
02AC2SOFTWAREALA A:96 , PHE A:97 , ASN A:98 , LEU A:101 , VAL A:105 , ASP A:159 , GLY A:161 , ALA A:162 , HIS A:256 , ILE A:258 , EDO A:411 , HOH A:589 , HOH A:647 , HOH A:662binding site for residue ADN A 402
03AC3SOFTWAREARG A:24 , LEU A:185 , LYS A:198 , ASN A:213binding site for residue ACT A 403
04AC4SOFTWARESER A:27 , LYS A:28 , ALA A:180 , LEU A:181 , ASP A:182 , HOH A:594 , HOH A:650binding site for residue ACT A 404
05AC5SOFTWAREGLU A:9 , ALA A:13binding site for residue ACT A 405
06AC6SOFTWAREARG A:85 , ARG A:279 , ASP A:282 , VAL A:308 , ARG A:340 , HOH A:668binding site for residue ACT A 406
07AC7SOFTWAREGLY A:190 , ILE A:192 , GLY A:215 , ILE A:216 , VAL A:237 , THR A:239 , HOH A:621binding site for residue ACT A 407
08AC8SOFTWAREGLU A:9 , TYR A:10 , SER A:11 , ARG A:12 , ALA A:13 , ARG A:22binding site for residue ACT A 408
09AC9SOFTWAREALA A:162 , ASN A:191 , THR A:239 , SER A:240 , GLU A:244 , HOH A:647binding site for residue EDO A 409
10AD1SOFTWAREVAL A:143 , ASP A:182 , GLY A:196 , ASP A:234 , ARG A:303 , HOH A:545binding site for residue EDO A 410
11AD2SOFTWAREVAL A:105 , ASN A:109 , PHE A:112 , ARG A:245 , HIS A:256 , ADN A:402binding site for residue EDO A 411
12AD3SOFTWAREPHE A:276 , ALA A:277 , PRO A:278 , GLY A:307 , ASP A:309 , HOH A:658binding site for residue EDO A 412
13AD4SOFTWAREALA A:103 , ARG A:129binding site for residue EDO A 413

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4XDR)

(-) 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:329
                                                                                                                                                                                                                                                                                                                                                                         
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeeeee..eeeeeeeee..hhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhh......eeehhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhh...hhhhhhhhhhhhhhh.eeeee.......eeeee...........hhhhhhhhhhhhhhhhh....eeeee..eeeee.........eeeee...........eeeee..eeeeeee....eeee..eeee................eeeeee.hhhhhhhhhhhhhhhhhhhhhhhhh.....eeeee....eeee...hhh.eee.....ee.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4xdr A   5 ARVREYSRAELVIGTLCRVRVYSKRPAAEVHAALEEVFTLLQQQEMVLSANRDDSALAALNAQAGSAPVVVDRSLYALLERALFFAEKSGGAFNPALGAVVKLWNIGFDRAAVPDPDALKEALTRCDFRQVHLRAGVSVGAPHTVQLAQAGMQLDLGAIAKGFLADKIVQLLTAHALDSALVDLGGNIFALGLKYGQRLEWNVGIRDPHGTGQKPALVVSVRDCSVVTSGAYERFFERDGVRYHHIIDPVTGFPAHTDVDSVSIFAPRSTDAAALATACFVLGYEKSCALLREFPGVDALFIFPDKRVRASAGIVDRVRVLDARFVLER 340
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194     ||211       221       231       241       251       261       271       281       291       301       311       321       331         
                                                                                                                                                                                                                             200|                                                                                                                                    
                                                                                                                                                                                                                              208
   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 4XDR)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) 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 ]
    ADN  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    EDO  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    MG  [ 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 ]
    AC8  [ RasMol ]  +environment [ RasMol ]
    AC9  [ RasMol ]  +environment [ RasMol ]
    AD1  [ RasMol ]  +environment [ RasMol ]
    AD2  [ RasMol ]  +environment [ RasMol ]
    AD3  [ RasMol ]  +environment [ RasMol ]
    AD4  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 4xdr)
 

(-) 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
  4xdr
    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
  APBE_TREPA | O83774
    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)
  2.7.1.180
    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
  APBE_TREPA | O83774
    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
        APBE_TREPA | O83774: 4ifu 4ifw 4ifx 4ifz 4ig1 4xdt 4xdu

(-) Related Entries Specified in the PDB File

4ifu 4IFU CONTAINS THE WILD TYPE PROTEIN, APO FORM.