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(-) Description

Title :  CRYSTAL STRUCTURE OF FUSED DOCKING DOMAINS FROM PIKAIII AND PIKAIV OF THE PIKROMYCIN POLYKETIDE SYNTHASE
 
Authors :  T. J. Buchholz, T. W. Geders, F. E. Bartley, K. A. Reynolds, J. L. Smith, D. H. Sherman
Date :  03 Nov 08  (Deposition) - 27 Jan 09  (Release) - 27 Jan 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.75
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Docking Domain, Polyketide Synthase, Pikromycin, H2-T2, Protein Binding (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  T. J. Buchholz, T. W. Geders, F. E. Bartley, K. A. Reynolds, J. L. Smith, D. H. Sherman
Structural Basis For Binding Specificity Between Subclasses Of Modular Polyketide Synthase Docking Domains.
Acs Chem. Biol. V. 4 41 2009
PubMed-ID: 19146481  |  Reference-DOI: 10.1021/CB8002607
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - TYPE I POLYKETIDE SYNTHASE PIKAIII, TYPE I POLYKETIDE SYNTHASE PIKAIV FUSION PROTEIN
    ChainsA, B
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPMCSG7
    Expression System StrainBL21(DE3)
    Expression System Taxid562
    Expression System Vector TypePLASMID
    FragmentC-TERMINAL DOMAIN OF PIKAIII FUSED TO N-TERMINAL DOMAIN OF PIKAIV
    GenePIKAIII, PIKAIV
    Organism ScientificSTREPTOMYCES VENEZUELAE
    Organism Taxid54571
    StrainATCC15439

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 1)

Asymmetric/Biological Unit (1, 1)
No.NameCountTypeFull Name
1NA1Ligand/IonSODIUM ION

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG B:28 , ASP B:31 , GLN B:34 , HOH B:44 , HOH B:140BINDING SITE FOR RESIDUE NA B1563

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3F5H)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3F5H)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3F5H)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3F5H)

(-) Exons   (0, 0)

(no "Exon" information available for 3F5H)

(-) 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:54
 aligned with PIKA3_STRVZ | Q9ZGI3 from UniProtKB/Swiss-Prot  Length:1562

    Alignment length:134
                                   503       513       523       533       543       553       563       573       583       593       603       613       623    
         PIKA3_STRVZ    494 ALDAQIGQLAAYADGRTDVDPAVAARALVDSRTAMEHRAVAVGDSREALRDALRMPEGLVRGTSSDVGRVAFVFPGQGTQWAGMGAELLDSSPEFAASMAECETALSRYVDWSLEAVVRQEPGAPTLDRVDVVQ  627
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhh--------------hhh----hhhhh--hhhhhhhhh-hhhhhhhhhhhhh------------------------------------------hhhhhhhh-------------hhhh----hhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------- Transcript
                3f5h A 1543 SID--------------DLD----AEALI--RMALGPRNT-MTSSNEQLVDALR------------------------------------------ASLKENEE-------------LRKE----SRRRADRRQ   34
                              |      -      1548    |   |- |    1562 |       9   |     -         -         -         -      | 17   |     -       |24|    |  30    
                              |           1546 | 1549   |  |    1562 1          13                                         14     21            22 25   26        
                           1545             1548     1553  |                                                                                                      
                                                        1554                                                                                                      

Chain A from PDB  Type:PROTEIN  Length:54
 aligned with PIKA4_STRVZ | Q9ZGI2 from UniProtKB/Swiss-Prot  Length:1346

    Alignment length:54
                                                1                                 
                                     -         -|       10        20        30    
         PIKA4_STRVZ      - --------------------MTSSNEQLVDALRASLKENEELRKESRRRADRRQ   34
               SCOP domains ------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------ Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------ Transcript
                3f5h A 1543 SIDDLDAEALIRMALGPRNTMTSSNEQLVDALRASLKENEELRKESRRRADRRQ   34
                                  1552      1562|       10        20        30    
                                            1562|                                 
                                                1                                 

Chain B from PDB  Type:PROTEIN  Length:57
 aligned with PIKA3_STRVZ | Q9ZGI3 from UniProtKB/Swiss-Prot  Length:1562

    Alignment length:141
                                   503       513       523       533       543       553       563       573       583       593       603       613       623       633 
         PIKA3_STRVZ    494 ALDAQIGQLAAYADGRTDVDPAVAARALVDSRTAMEHRAVAVGDSREALRDALRMPEGLVRGTSSDVGRVAFVFPGQGTQWAGMGAELLDSSPEFAASMAECETALSRYVDWSLEAVVRQEPGAPTLDRVDVVQPVTFAVM  634
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhh--------------hhh----hhhhh--hhhhhhhhh-hhhhhhhhhhhhh-------------------------------hhhhhh--------hhhhhhhhhhhhh------hhh.------------------. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                3f5h B 1543 SID--------------DLD----AEALI--RMALGPRNT-MTSSNEQLVDALR-------------------------------ASLKEN--------EELRKESRRRADR------RQEP------------------M   37
                              |      -      1548    |   |- |    1562 |       9   |     -         -         -     |  18|       20        30 |      34 |       -         -|
                           1545           1546 | 1549   |  |    1562 1          13                              14   19       20          32     33 36                 37
                                            1548     1553  |                                                                                                             
                                                        1554                                                                                                             

Chain B from PDB  Type:PROTEIN  Length:57
 aligned with PIKA4_STRVZ | Q9ZGI2 from UniProtKB/Swiss-Prot  Length:1346

    Alignment length:57
                                                1                                    
                                     -         -|       10        20        30       
         PIKA4_STRVZ      - --------------------MTSSNEQLVDALRASLKENEELRKESRRRADRRQEPM   37
               SCOP domains --------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------- Transcript
                3f5h B 1543 SIDDLDAEALIRMALGPRNTMTSSNEQLVDALRASLKENEELRKESRRRADRRQEPM   37
                                  1552      1562|       10        20        30       
                                            1562|                                    
                                                1                                    

   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 3F5H)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3F5H)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3F5H)

(-) Gene Ontology  (9, 15)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (PIKA3_STRVZ | Q9ZGI3)
molecular function
    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:0048037    cofactor binding    Interacting selectively and non-covalently with a cofactor, a substance that is required for the activity of an enzyme or other protein. Cofactors may be inorganic, such as the metal atoms zinc, iron, and copper in certain forms, or organic, in which case they are referred to as coenzymes. Cofactors may either be bound tightly to active sites or bind loosely with the substrate.
    GO:0031177    phosphopantetheine binding    Interacting selectively and non-covalently with phosphopantetheine, the vitamin pantetheine 4'-(dihydrogen phosphate).
    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.
    GO:0016747    transferase activity, transferring acyl groups other than amino-acyl groups    Catalysis of the transfer of an acyl group, other than amino-acyl, from one compound (donor) to another (acceptor).
biological process
    GO:0033068    macrolide biosynthetic process    The chemical reactions and pathways leading to the formation of macrolides, any of a large group of polyketide compounds that contain a large lactone ring with few or no double bonds and no nitrogen atoms, linked glycosidically to one or more sugar groups. The macrolides include the carbomycins, the erythromycins, oleandomycin, oligomycins, and the spiramycins, and act as antibiotics, mainly against Gram-positive bacteria.
    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.

Chain A,B   (PIKA4_STRVZ | Q9ZGI2)
molecular function
    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:0016788    hydrolase activity, acting on ester bonds    Catalysis of the hydrolysis of any ester bond.
    GO:0031177    phosphopantetheine binding    Interacting selectively and non-covalently with phosphopantetheine, the vitamin pantetheine 4'-(dihydrogen phosphate).
    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.
    GO:0016747    transferase activity, transferring acyl groups other than amino-acyl groups    Catalysis of the transfer of an acyl group, other than amino-acyl, from one compound (donor) to another (acceptor).
biological process
    GO:0009058    biosynthetic process    The chemical reactions and pathways resulting in the formation of substances; typically the energy-requiring part of metabolism in which simpler substances are transformed into more complex ones.
    GO:0033068    macrolide biosynthetic process    The chemical reactions and pathways leading to the formation of macrolides, any of a large group of polyketide compounds that contain a large lactone ring with few or no double bonds and no nitrogen atoms, linked glycosidically to one or more sugar groups. The macrolides include the carbomycins, the erythromycins, oleandomycin, oligomycins, and the spiramycins, and act as antibiotics, mainly against Gram-positive bacteria.
    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.

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 Related Entries

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

UniProtKB/Swiss-Prot
        PIKA4_STRVZ | Q9ZGI21mn6 1mna 1mnq 2h7x 2h7y 2hfj 2hfk

(-) Related Entries Specified in the PDB File

1pzr STRUCTURE OF FUSED DOCKING DOMAINS FROM THE ERYTHROMYCIN POLYKETIDE SYNTHASE (DEBS), A MODEL FOR THE INTERACTION BETWEEN DEBS 2 AND DEBS 3: THE A DOMAIN