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

(-) Description

Title :  CRYSTAL STRUCTURE OF MYCOBACTERIUM TUBERCULOSIS PKS11 IN COMPLEX WITH POLYKETIDE INTERMEDIATES AND EVIDENCE THAT IT SYNTHESIZE ALKYLPYRONES
 
Authors :  K. Gokulan, J. C. Sacchettini, Mycobacterium Tuberculosis Structu Proteomics Project (Xmtb)
Date :  19 Feb 13  (Deposition) - 24 Apr 13  (Release) - 27 Nov 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.98
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
Keywords :  Lipid Biosynthesis, Structural Genomics, Enzyme Function Initiative, Ketosynthase Enzyme, Alkylpyrone Synthesis, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  K. Gokulan, S. E. O'Leary, W. K. Russell, D. H. Russell, M. Lalgondar, T. P. Begley, T. R. Ioerger, J. C. Sacchettini
Crystal Structure Of Mycobacterium Tuberculosis Polyketide Synthase 11 (Pks11) Reveals Intermediates In The Synthesis Of Methyl-Branched Alkylpyrones.
J. Biol. Chem. V. 288 16484 2013
PubMed-ID: 23615910  |  Reference-DOI: 10.1074/JBC.M113.468892

(-) Compounds

Molecule 1 - ALPHA-PYRONE SYNTHESIS POLYKETIDE SYNTHASE-LIKE PKS11
    Chains: A, C, B, D
    EC Number: 2.3.1.-
    Engineered: YES
    Expression System: MYCOBACTERIUM SMEGMATIS
    Expression System Taxid: 1772
    Expression System Vector Type: P1601-DEST17
    Gene: PKS11, RV1665, MT1705
    Organism Scientific: MYCOBACTERIUM TUBERCULOSIS
    Organism Taxid: 1773
    Strain: H37RV
    Synonym: ALPHA-PYRONE SYNTHESIS POLYKETIDE SYNTHASE TYPE III PKS11, CHALCONE SYNTHASE-LIKE PROTEIN, CHS-LIKE

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): AB  
Biological Unit 2 (1x):   CD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 4JAR)

(-) Sites  (0, 0)

(no "Site" information available for 4JAR)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (9, 9)

Asymmetric Unit
No.Residues
1Val A:111 -Pro A:112
2Phe A:134 -Gly A:135
3Gly A:342 -Phe A:343
4Val C:111 -Pro C:112
5Gly C:342 -Phe C:343
6Val B:111 -Pro B:112
7Gly B:342 -Phe B:343
8Val D:111 -Pro D:112
9Gly D:342 -Phe D:343

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4JAR)

(-) 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:352
                                                                                                                                                                                                                                                                                                                                                                                                
               SCOP domains d4jara1 A:2-211 automated matches                                                                                                                                                                                 d4jara2 A:212-353 automated matches                                                                                                            SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeee.....eehhhhhhhhh...hhhhhhhhhhhhhhh....ee....hhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhh.eeeee........hhhhhhhhhh......eeeee.....hhhhhhhhhhhhhhh.....eeeeeeeee.hhhhhhh..hhhhhhhhhhh.eeeeeeeeehhhhhh.......eeeeeeeee...hhh.eeeeee..eeeeee...hhhhhhhhhhhhhhhhhhhh..hhh.eeeeee...hhhhhhhhhhhhh.....hhhhhhhhhhh..hhhhhhhhhhhhhhhh......eeeeeeee...eeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4jar A   2 SVIAGVFGALPPHRYSQSEITDSFVEFPGLKEHEEIIRRLHAAAKVNGRHLVLPLQQYPSLTDFGDANEIFIEKAVDLGVEALLGALDDANLRPSDIDMIATATVTGVAVPSLDARIAGRLGLRPDVRRMPLFGLGCVAGAAGVARLRDYLRGAPDDVAVLVSVELCSLTYPAVKPTVSSLVGTALFGDGAAAVVAVGDRRAEQVRAGGPDILDSRSSLYPDSLHIMGWDVGSHGLRLRLSPDLTNLIERYLANDVTTFLDAHRLTKDDIGAWVSHPGGPKVIDAVATSLALPPEALELTWRSLGEIGNLSSASILHILRDTIEKRPPSGSAGLMLAMGPGFCTELVLLRWR 353
                                    11        21        31        41        51        61        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       341       351  


Chain B from PDB  Type:PROTEIN  Length:353
                                                                                                                                                                                                                                                                                                                                                                                                 
               SCOP domains d4jarb1 B:1-211 automated matches                                                                                                                                                                                  d4jarb2 B:212-353 automated matches                                                                                                            SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeeee...eeeehhhhhhhhh....hhhhhhhhhhhhhhh...eeee..hhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhh.eeeeee.......hhhhhhhhhhh.....eeeeee.hhhhhhhhhhhhhhhhhhh....eeeeeeeee.hhhhhhh..hhhhhhhhhhh.eeeeeeeeehhhhhhhh.....eeeeeeeee...hhh.eeeeee..eeeeee..hhhhhhhhhhhhhhhhhhhh.......eeeeee...hhhhhhhhhhhh......hhhhhhhhhhhh.hhhhhhhhhhhhhhhh......eeeeeeee...eeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4jar B   1 MSVIAGVFGALPPHRYSQSEITDSFVEFPGLKEHEEIIRRLHAAAKVNGRHLVLPLQQYPSLTDFGDANEIFIEKAVDLGVEALLGALDDANLRPSDIDMIATATVTGVAVPSLDARIAGRLGLRPDVRRMPLFGLGCVAGAAGVARLRDYLRGAPDDVAVLVSVELCSLTYPAVKPTVSSLVGTALFGDGAAAVVAVGDRRAEQVRAGGPDILDSRSSLYPDSLHIMGWDVGSHGLRLRLSPDLTNLIERYLANDVTTFLDAHRLTKDDIGAWVSHPGGPKVIDAVATSLALPPEALELTWRSLGEIGNLSSASILHILRDTIEKRPPSGSAGLMLAMGPGFCTELVLLRWR 353
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350   


Chain C from PDB  Type:PROTEIN  Length:352
                                                                                                                                                                                                                                                                                                                                                                                                
               SCOP domains d4jarc1 C:2-211 automated matches                                                                                                                                                                                 d4jarc2 C:212-353 automated matches                                                                                                            SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeee....eeehhhhhhhhh....hhhhhhhhhhhhhh....eee...hhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhh.eeeee........hhhhhhhhhhh.....eeeee..hhhhhhhhhhhhhhhhhh.....eeeeeeeee.hhhhhhh..hhhhhhhhhhh.eeeeeeeeehhhhhhhhh....eeeeeeeee...hhh.eeeeee..eeeeee..hhhhhhhhhhhhhhhhhhhh.......eeeeee...hhhhhhhhhhhh......hhhhhhhhhhhh...hhhhhhhhhhhhh.......eeeeeeee...eeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4jar C   2 SVIAGVFGALPPHRYSQSEITDSFVEFPGLKEHEEIIRRLHAAAKVNGRHLVLPLQQYPSLTDFGDANEIFIEKAVDLGVEALLGALDDANLRPSDIDMIATATVTGVAVPSLDARIAGRLGLRPDVRRMPLFGLGCVAGAAGVARLRDYLRGAPDDVAVLVSVELCSLTYPAVKPTVSSLVGTALFGDGAAAVVAVGDRRAEQVRAGGPDILDSRSSLYPDSLHIMGWDVGSHGLRLRLSPDLTNLIERYLANDVTTFLDAHRLTKDDIGAWVSHPGGPKVIDAVATSLALPPEALELTWRSLGEIGNLSSASILHILRDTIEKRPPSGSAGLMLAMGPGFCTELVLLRWR 353
                                    11        21        31        41        51        61        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       341       351  


Chain D from PDB  Type:PROTEIN  Length:352
                                                                                                                                                                                                                                                                                                                                                                                                
               SCOP domains d4jard1 D:2-211 automated matches                                                                                                                                                                                 d4jard2 D:212-353 automated matches                                                                                                            SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeee....eeehhhhhhhhh....hhhhhhhhhhhhhhh...eee...hhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhh.eeeee........hhhhhhhhhhh.....eeeee..hhhhhhhhhhhhhhhhhh.....eeeeeeeee.hhhhhhh..hhhhhhhhhhh.eeeeeeeee.............eeeeeeeee.......eeeeee..eeeeee...hhhhhhhhhhhhhhhhh.........eeeeee...hhhhhhhhhhhh......hhhhhhhhhhhh.hhhhhhhhhhhhhhhhh.....eeeeeeee...eeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4jar D   2 SVIAGVFGALPPHRYSQSEITDSFVEFPGLKEHEEIIRRLHAAAKVNGRHLVLPLQQYPSLTDFGDANEIFIEKAVDLGVEALLGALDDANLRPSDIDMIATATVTGVAVPSLDARIAGRLGLRPDVRRMPLFGLGCVAGAAGVARLRDYLRGAPDDVAVLVSVELCSLTYPAVKPTVSSLVGTALFGDGAAAVVAVGDRRAEQVRAGGPDILDSRSSLYPDSLHIMGWDVGSHGLRLRLSPDLTNLIERYLANDVTTFLDAHRLTKDDIGAWVSHPGGPKVIDAVATSLALPPEALELTWRSLGEIGNLSSASILHILRDTIEKRPPSGSAGLMLAMGPGFCTELVLLRWR 353
                                    11        21        31        41        51        61        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       341       351
   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  (1, 8)

Asymmetric Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)
(-)
Fold: Thiolase-like (231)
(-)
Superfamily: Thiolase-like (231)
(-)
Family: automated matches (108)
(-)
Protein domain: automated matches (108)
(-)
Mycobacterium tuberculosis [TaxId: 1773] (11)
1ad4jara1A:2-211
1bd4jara2A:212-353
1cd4jarb1B:1-211
1dd4jarb2B:212-353
1ed4jarc1C:2-211
1fd4jarc2C:212-353
1gd4jard1D:2-211
1hd4jard2D:212-353

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (12, 21)

Asymmetric Unit(hide GO term definitions)

 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
(no "Ligands, Modified Residues, Ions" information available for 4jar)
 
  Sites
(no "Sites" information available for 4jar)
 
  Cis Peptide Bonds
    Gly A:342 - Phe A:343   [ RasMol ]  
    Gly B:342 - Phe B:343   [ RasMol ]  
    Gly C:342 - Phe C:343   [ RasMol ]  
    Gly D:342 - Phe D:343   [ RasMol ]  
    Phe A:134 - Gly A:135   [ RasMol ]  
    Val A:111 - Pro A:112   [ RasMol ]  
    Val B:111 - Pro B:112   [ RasMol ]  
    Val C:111 - Pro C:112   [ RasMol ]  
    Val D:111 - Pro D:112   [ 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 | Biol. Unit 1 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
  4jar
    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
  PKS11_MYCTO | P9WPF2
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
  PKS11_MYCTU | P9WPF3
    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)
  2.3.1.-
    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
  PKS11_MYCTO | P9WPF2
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)
  PKS11_MYCTU | P9WPF3
    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
        PKS11_MYCTO | P9WPF2: 4jao 4jap 4jaq 4jat 4jd3
        PKS11_MYCTU | P9WPF3: 4jao 4jap 4jaq 4jat 4jd3

(-) Related Entries Specified in the PDB File

4jao 4jap 4jaq 4jat 4jd3