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 CERJ FROM STREPTOMYCES TENDAE
 
Authors :  G. Zocher, C. Hertweck, T. Bretschneider, T. Stehle
Date :  18 May 11  (Deposition) - 21 Dec 11  (Release) - 07 May 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Acyltransferase, Fabh Homologue, Ks Iii Homologue, Dimethyl Malonyl Transfer, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  T. Bretschneider, G. Zocher, M. Unger, K. Scherlach, T. Stehle, C. Hertweck
A Ketosynthase Homolog Uses Malonyl Units To Form Esters In Cervimycin Biosynthesis.
Nat. Chem. Biol. V. 8 154 2011
PubMed-ID: 22179067  |  Reference-DOI: 10.1038/NCHEMBIO.746

(-) Compounds

Molecule 1 - CERJ
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Organism Scientific: STREPTOMYCES TENDAE
    Organism Taxid: 1932

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 8)

Asymmetric/Biological Unit (2, 8)
No.NameCountTypeFull Name
1ACT4Ligand/IonACETATE ION
2CL4Ligand/IonCHLORIDE ION

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELEU A:84 , ARG A:115 , TYR A:164 , HOH A:571 , HOH B:519BINDING SITE FOR RESIDUE ACT A 401
2AC2SOFTWARETRP A:3 , GLU A:4 , ASN A:5 , HOH A:582 , HOH A:585BINDING SITE FOR RESIDUE ACT A 402
3AC3SOFTWAREHOH A:568 , LEU B:84 , ARG B:115 , TYR B:164 , HOH B:517BINDING SITE FOR RESIDUE ACT B 401
4AC4SOFTWARETRP B:3 , GLU B:4 , ASN B:5 , HOH B:396BINDING SITE FOR RESIDUE ACT B 402
5AC5SOFTWAREASP B:215 , ARG B:219 , HOH B:484BINDING SITE FOR RESIDUE CL B 358
6AC6SOFTWAREARG B:34 , ARG B:38 , HOH B:384BINDING SITE FOR RESIDUE CL B 359
7AC7SOFTWAREARG A:152 , ASP A:215 , ARG A:219 , HOH A:583BINDING SITE FOR RESIDUE CL A 358
8AC8SOFTWAREARG A:34 , ARG A:38BINDING SITE FOR RESIDUE CL A 359

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3S3L)

(-) Cis Peptide Bonds  (6, 6)

Asymmetric/Biological Unit
No.Residues
1Gly A:150 -Pro A:151
2Glu A:209 -Pro A:210
3Gly A:328 -Tyr A:329
4Gly B:150 -Pro B:151
5Glu B:209 -Pro B:210
6Gly B:328 -Tyr B:329

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3S3L)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3S3L)

(-) Exons   (0, 0)

(no "Exon" information available for 3S3L)

(-) 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:342
 aligned with H2L2M1_STRTE | H2L2M1 from UniProtKB/TrEMBL  Length:357

    Alignment length:342
                                    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  
         H2L2M1_STRTE     1 MRWENLFVSGVAAWLPPLSTAQDAVMAGLLDPARSKLRGIESVTVASDAEEDAPPRMAARAARAALGRGDVDPADVSLVLHSSLWFQGIDLWPAASYVAHEAVGRHVPAFGLAQRCNGGMGAIELAGAYLGSGIGAGHAALLTTGDRFAGPRIDRWNSVDVTMYGDGAAALVLSTRDGFARVLSTATGVDNSLEILARGDEPFAPHPVEPSPVADLGTRTVRGAELADLPDLTHRYIDLLVAAKTQALEDAGTAIEDIAHAVIPVSRRGTGHELHDLLGLPDERTSWAYGRTTGHVGAGDQYAGLAHLVENALVQPGDRVLLFGGGAGYTCTAAVVEILRMP 342
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ......eeeeeeee...eeehhhhhhh...hhhhhhhhh..eee....hhhhhhhhhhhhhhhhhhhhh..hhh.eeeeeee..........hhhhhhhhhhh.....eeeeehhhhhhhhhhhhhhhhhhh......eeeeeeee....................eeeeeeee.....eeeeeeeeee.hhhhhhhh................hhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhh..hhhhh.eee..........hhhhhhh.hhhhhhhhhhhhhh....hhhhhhhhhhhhh.......eeeee......eeeeeeeee.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3s3l A   1 MRWENLFVSGVAAWLPPLSTAQDAVMAGLLDPARSKLRGIESVTVASDAEEDAPPRMAARAARAALGRGDVDPADVSLVLHSSLWFQGIDLWPAASYVAHEAVGRHVPAFGLAQRCNGGMGAIELAGAYLGSGIGAGHAALLTTGDRFAGPRIDRWNSVDVTMYGDGAAALVLSTRDGFARVLSTATGVDNSLEILARGDEPFAPHPVEPSPVADLGTRTVRGAELADLPDLTHRYIDLLVAAKTQALEDAGTAIEDIAHAVIPVSRRGTGHELHDLLGLPDERTSWAYGRTTGHVGAGDQYAGLAHLVENALVQPGDRVLLFGGGAGYTCTAAVVEILRMP 342
                                    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  


Chain B from PDB  Type:PROTEIN  Length:342
 aligned with H2L2M1_STRTE | H2L2M1 from UniProtKB/TrEMBL  Length:357

    Alignment length:342
                                    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  
         H2L2M1_STRTE     1 MRWENLFVSGVAAWLPPLSTAQDAVMAGLLDPARSKLRGIESVTVASDAEEDAPPRMAARAARAALGRGDVDPADVSLVLHSSLWFQGIDLWPAASYVAHEAVGRHVPAFGLAQRCNGGMGAIELAGAYLGSGIGAGHAALLTTGDRFAGPRIDRWNSVDVTMYGDGAAALVLSTRDGFARVLSTATGVDNSLEILARGDEPFAPHPVEPSPVADLGTRTVRGAELADLPDLTHRYIDLLVAAKTQALEDAGTAIEDIAHAVIPVSRRGTGHELHDLLGLPDERTSWAYGRTTGHVGAGDQYAGLAHLVENALVQPGDRVLLFGGGAGYTCTAAVVEILRMP 342
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ......eeeeeeee...eeehhhhhhh...hhhhhhhhh..eee....hhhhhhhhhhhhhhhhhhhhh..hhh.eeeeeee..........hhhhhhhhhhh.....eeeeehhhhhhhhhhhhhhhhhhh......eeeeeeee....................eeeeeeee.....eeeeeeeeee.hhhhhhhh................hhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhh..hhh.eeeee..........hhhhhhh.hhhhhhhhhhhhhh.hhhhhhhhhhhhhhhh.......eeeee......eeeeeeeee.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3s3l B   1 MRWENLFVSGVAAWLPPLSTAQDAVMAGLLDPARSKLRGIESVTVASDAEEDAPPRMAARAARAALGRGDVDPADVSLVLHSSLWFQGIDLWPAASYVAHEAVGRHVPAFGLAQRCNGGMGAIELAGAYLGSGIGAGHAALLTTGDRFAGPRIDRWNSVDVTMYGDGAAALVLSTRDGFARVLSTATGVDNSLEILARGDEPFAPHPVEPSPVADLGTRTVRGAELADLPDLTHRYIDLLVAAKTQALEDAGTAIEDIAHAVIPVSRRGTGHELHDLLGLPDERTSWAYGRTTGHVGAGDQYAGLAHLVENALVQPGDRVLLFGGGAGYTCTAAVVEILRMP 342
                                    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
   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 3S3L)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3S3L)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3S3L)

(-) Gene Ontology  (5, 5)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (H2L2M1_STRTE | H2L2M1)
molecular function
    GO:0004315    3-oxoacyl-[acyl-carrier-protein] synthase activity    Catalysis of the reaction: acyl-[acyl-carrier protein] + malonyl-[acyl-carrier protein] = 3-oxoacyl-[acyl-carrier protein] + CO2 + [acyl-carrier protein].
    GO:0003824    catalytic activity    Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
    GO:0016740    transferase activity    Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
biological process
    GO:0006633    fatty acid biosynthetic process    The chemical reactions and pathways resulting in the formation of a fatty acid, any of the aliphatic monocarboxylic acids that can be liberated by hydrolysis from naturally occurring fats and oils. Fatty acids are predominantly straight-chain acids of 4 to 24 carbon atoms, which may be saturated or unsaturated; branched fatty acids and hydroxy fatty acids also occur, and very long chain acids of over 30 carbons are found in waxes.
    GO:0008152    metabolic process    The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation.

 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 ]
    CL  [ 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 ]
 
  Cis Peptide Bonds
    Glu A:209 - Pro A:210   [ RasMol ]  
    Glu B:209 - Pro B:210   [ RasMol ]  
    Gly A:150 - Pro A:151   [ RasMol ]  
    Gly A:328 - Tyr A:329   [ RasMol ]  
    Gly B:150 - Pro B:151   [ RasMol ]  
    Gly B:328 - Tyr B:329   [ 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
  3s3l
    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
  H2L2M1_STRTE | H2L2M1
    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
  H2L2M1_STRTE | H2L2M1
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/TrEMBL
        H2L2M1_STRTE | H2L2M1: 3t5y 3t6s 3t8e

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 3S3L)