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 :  ENTF, A TERMINAL NONRIBOSOMAL PEPTIDE SYNTHETASE MODULE BOUND TO THE NON-NATIVE MBTH-LIKE PROTEIN PA2412
 
Authors :  B. R. Miller, A. M. Gulick
Date :  11 Apr 16  (Deposition) - 14 Sep 16  (Release) - 16 Nov 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.00
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Nonribosomal Peptide Synthetase, Nrps, Condensation, Adenylation, Pcp, Thioesterase, Mbth-Like Protein, Phosphopantetheine, Biosynthetic Protein, Ligase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  B. R. Miller, E. J. Drake, C. Shi, C. C. Aldrich, A. M. Gulick
Structures Of A Nonribosomal Peptide Synthetase Module Boun To Mbth-Like Proteins Support A Highly Dynamic Domain Architecture.
J. Biol. Chem. V. 291 22559 2016
PubMed-ID: 27597544  |  Reference-DOI: 10.1074/JBC.M116.746297
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - ENTEROBACTIN SYNTHASE COMPONENT F
    Chains: A
    EC Number: 2.7.7.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PET15B
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: ENTF, B0586, JW0578
    Organism Scientific: ESCHERICHIA COLI (STRAIN K12)
    Organism Taxid: 83333
    Strain: K12
    Synonym: ENTEROCHELIN SYNTHASE F,SERINE-ACTIVATING ENZYME,SERYL-AMP LIGASE
    Variant: W3110
 
Molecule 2 - MBTH-LIKE PROTEIN PA2412
    Chains: B
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PET15B
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: PA2412
    Organism Scientific: PSEUDOMONAS AERUGINOSA (STRAIN ATCC 15692 / PAO1 / 1C / PRS 101 / LMG 12228)
    Organism Taxid: 208964
    Strain: ATCC 15692 / PAO1 / 1C / PRS 101 / LMG 12228

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 3)

Asymmetric/Biological Unit (2, 3)
No.NameCountTypeFull Name
175C1Ligand/Ion5'-({[(2R,3S)-3-AMINO-4-HYDROXY-2-{[2-({N-[(2R)-2-HYDROXY-3,3-DIMETHYL-4-(PHOSPHONOOXY)BUTANOYL]-BETA-ALANYL}AMINO)ETHYL]SULFANYL}BUTYL]SULFONYL}AMINO)-5'-DEOXYADENOSINE
2BU92Ligand/IonMESO-2,3-BUTANEDIOL

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREPHE A:647 , ASP A:648 , ARG A:673 , VAL A:693 , SER A:722 , GLY A:723 , GLU A:724 , ALA A:725 , ASN A:744 , LEU A:745 , TYR A:746 , GLY A:747 , THR A:749 , VAL A:753 , ASP A:754 , ASP A:840 , TYR A:852 , ARG A:855 , LYS A:861 , ARG A:863 , GLY A:864 , GLN A:865 , ARG A:866 , SER A:1006 , HOH A:1410binding site for residue 75C A 1301
2AC2SOFTWARESER A:606 , LYS A:611 , SER A:822 , ARG A:823 , ARG A:837binding site for residue BU9 A 1302
3AC3SOFTWARELEU A:109 , ARG A:110 , SER A:113 , LYS A:115 , PRO A:116 , ARG A:135binding site for residue BU9 A 1303

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5JA2)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Gly A:340 -Asp A:341

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5JA2)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5JA2)

(-) Exons   (0, 0)

(no "Exon" information available for 5JA2)

(-) 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:1238
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..........eeeeeeeeee..hhhhhhhhhhhhhhhh.....eee..eee..........eeee.....hhhhhhhhhhhhhhh............eeeeee....eeeeeeeee.......hhhhhhhhhhhhhhhhhh..........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....................eeeeeeee..hhhhhhhhhh...hhhhhhhhhhhhhhhhhh...eeeeeeeee...hhhhhh.....eeeeeeeee.....hhhhhhhhhhhhhhhhhh....hhhhhhhhh.........eeee............eeeeeeeee......eeeeeee.....eeeeeeee....hhhhhhhhhhhhhhhhhhhhhh...........hhhhhhhhhhhh.........hhhhhhhhhhhhh...eeee....eeehhhhhhhhhhhhhhhhhh......eeeee...hhhhhhhhhhhhhh..eeee.....hhhhhhhhhhhhh..eeee...hhhhhh......eee....................eeeeeee.......eeeeeehhhhhhhhhhhhhhh......eeee.....hhhhhhhhhhhhh...eeee.......hhhhhhhhhhhhh..eeeehhhhhhhhhhh.hhhhhhhhhhhh.eeee....eehhhhhhhhhhh...eeeee.hhhhh...eeee.hhhhhhh....ee...ee...eeeeee............eeeeeee.....ee..hhhhhhhheee.......eeeeeeeeeee.....eeeeee...eeee..eeeehhhhhhhhh......eeeeeee..hhhhh......eeeeeee.......hhhhhhhhhh...hhhhh..eeee...........................hhhhhhhhhhhhhh...............hhhhhhhhhhhhhhhh....hhhhhhhh.hhhhhhhhhh......eeeee.....eeee.......hhhhhhhh.......eeeee......hhhhhh........hhhhhhh.......eeeeeehhhhhhhhhhhhhhhh...eeeeeee........hhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhh..........eeeeee........hhhhhh....eeeeee....hhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                5ja2 A   18 EKLSELPSAWSVAHYVELTGEVDSPLLARAVVAGLAQADTLRMRFTEVWQWVDDALTFELPEIIDLRTNIDPHGTAQALMQADLQQDLRVDSGKPLVFHQLIQVADNRWYWYQRYHHLLVDGFSFPAITRQIANIYCTWLRGEPTPASPFTPFADVVEEYQQYRESEAWQRDAAFWAEQRRQLPPPASLSPAPLPGRSASADILRLKLEFTDGEFRQLATQLSGVQRTDLALALAALWLGRLCNRMDYAAGFIFMRRLGSAALTATGPVLNVLPLGIHIAAQETLPELATRLAAQLKKMRRHQRYDAEQIVRDSAAGDEPLFGPVLNIKVFDYQLDIPDVQAQTHTLATGPVNDLELALFPDVHGDLSIEILANKQRYDEPTLIQHAERLKMLIAQFAADPALLCGDVDIMLPGEYAQLAQLNATQVEIPETTLSALVAEQAAKTPDAPALADARYLFSYREMREQVVALANLLRERGVKPGDSVAVALPRSVFLTLALHAIVEAGAAWLPLDTGYPDDRLKMMLEDARPSLLITTDDQLPRFSDVPNLTSLCYNAPLTPQGSAPLQLSQPHHTAYIIFTSGSTGRPKGVMVGQTAIVNRLLWMQNHYPLTGEDVVAQKTPCSFDVSVWEFFWPFIAGAKLVMAEPEAHRDPLAMQQFFAEYGVTTTHFVPSMLAAFVASLTPQTARQSCATLKQVFCSGEALPADLCREWQQLTGAPLHNLYGPTEAAVDVSWYPAFGEELAQVRGSSVPIGYPVWNTGLRILDAMMHPVPPGVAGDLYLTGIQLAQGYLGRPDLTASRFIADPFAPGERMYRTGDVARWLDNGAVEYLGRSDDQLKIRGQRIELGEIDRVMQALPDVEQAVTHACVINQAAATGGDARQLVGYLVSQSGLPLDTSALQAQLRETLPPHMVPVVLLQLPQLPLSANGKLDRKALPLPELAPKAGSETIIAAAFSSLLGCDVQDADADFFALGGHSLLAMKLAAQLSRQVARQVTPGQVMVASTVAKLATIIDRMGFETILPLREGNGPTLFCFHPASGFAWQFSVLSRYLDPQWSIIGIQSPRPNGPMQTAANLDEVCEAHLATLLEQQPHGPYYLLGYSLGGTLAQGIAARLRAREQVAFLGLLDTWPPETLDPEVLAEINREREAFLAAQQGELFTTIEGNYADAVRLLTTAHSVPFDGKATLFVAERTLQEGMSPERAWSPWELDIYRQDCAHVDIISPGTFEKIGPIIRATLN 1292
                                    27        37        47        57      ||71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331   ||  343       353       363       373       383       393       403       413       423       433       443       453       463       473       483       493       503       513       523       533       543       553       563       573       583       593       603       613       623       633       643       653       663       673       683       693       703       713       723       733       743       753       763       773       783       793       803       813       823       833       843       853       863       873       883       893       903       913       923       933       943       953       963|      980       990      1000      1010      1020      1030      1040  ||  1057      1067      1077      1087      1097      1107      1117      1127      1137      1147      1158      1168  ||  1188      1198    ||1212      1222      1232      1242      1252     |1264      1274      1284        
                                                                         64|                                                                                                                                                                                                                                                                       335|                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              963|                                                                    1043|                                                                                                   1154|           1171|                 1203|                                              1258|                               
                                                                          69                                                                                                                                                                                                                                                                        338                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               971                                                                     1051                                                                                                    1156            1182                  1208                                               1261                               


Chain B from PDB  Type:PROTEIN  Length:68
                                                                                                     
               SCOP domains -------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhh...eeeeee.....eeeee.........eeeeeeeehhhhhhhhhhhh....hhhhh... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------- Transcript
                5ja2 B    0 HMTSVFDRDDIQFQVVVNHEEQYSIWPEYKEIPQGWRAAGKSGLKKDCLAYIEEVWTDMRPLSLRQHM   67
                                     9        19        29        39        49        59
   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 5JA2)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5JA2)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5JA2)

(-) Gene Ontology  (16, 16)

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
    75C  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    BU9  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Gly A:340 - Asp A:341   [ 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
  5ja2
    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
  ENTF_ECOLI | P11454
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
  Q9I169_PSEAE | Q9I169
    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)
  2.7.7.-
    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
  ENTF_ECOLI | P11454
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)
  Q9I169_PSEAE | Q9I169
    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
        ENTF_ECOLI | P11454: 2roq 3tej 5ja1 5t3d
UniProtKB/TrEMBL
        Q9I169_PSEAE | Q9I169: 2gpf 2pst

(-) Related Entries Specified in the PDB File

5ja2