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 THE DEHYDRATASE DOMAIN OF RZXB FROM PSEUDOMONAS FLUORESCENS
 
Authors :  R. P. Jakob, D. A. Herbst, T. Maier
Date :  04 Mar 16  (Deposition) - 29 Mar 17  (Release) - 29 Mar 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Polyketide, Macrolactin, Trans-At, Pks, At-Less, Dehydratase, Rhizoxin, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  R. P. Jakob, R. Muller, D. A. Herbst, T. Maier
Crystal Structures Of Dehydratase Domains From Trans-At Polyketide Biosynthetic Pathway
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - POLYKETIDE SYNTHASE/NONRIBOSOMAL PEPTIDE SYNTHETASE HYBRID RZXB
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PNIC28-BSA4
    Expression System Taxid: 469008
    Fragment: UNP RESIDUES 1231-1540
    Gene: RZXB, PFL_2989
    Organism Scientific: PSEUDOMONAS FLUORESCENS (STRAIN PF-5 / ATCC BAA-477)
    Organism Taxid: 220664
    Strain: PF-5 / ATCC BAA-477

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): A 
Biological Unit 2 (1x):  B

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 5IL6)

(-) Sites  (0, 0)

(no "Site" information available for 5IL6)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5IL6)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Ala A:4617 -Pro A:4618
2Ala B:4617 -Pro B:4618

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5IL6)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5IL6)

(-) Exons   (0, 0)

(no "Exon" information available for 5IL6)

(-) 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:275
                                                                                                                                                                                                                                                                                                                    
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........ee......eeeeee....hhhhhheee..ee..hhhhhhhhhhhhhhhhh........eeeeeeeee............eeeeeeeeee..eeeeeeeee.....eeeeeeeeeeee..............eeehhhhhhhhhhhhheee.hhhh.eeeeeee..eeeeeee..hhhhhh....hhhhhhhhhhhhhhhh...........eeeeeeeeee......eeeeeeeee......eeeeeeee.....eeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                5il6 A 4370 EHLHPLLHRNVSDLRGLRYLSRFSGDESVLAEHRVNGQAVLAGAAMIVMIQAALTDALGGAVPAGRGLVISDLSWRQPFSVDAANNGELFLELSMPAAGDYRIGIYAYDQAAQLQLHCQARASTAEVQAAWLDFSSLGAQVVDVEACYQRFAAMGIEYGAGHRRLLSLVRQGDQALARIALQDPALNSGFALHPALLDAAMQGVMALLLDELEERPALLLPAGLGQCVLLADCPASLQVQIRRAPSTAPDYCFDLALFDDQGQCCAILNQLSFQP 4644
                                  4379      4389      4399      4409      4419      4429      4439      4449      4459      4469      4479      4489      4499      4509      4519      4529      4539      4549      4559      4569      4579      4589      4599      4609      4619      4629      4639     


Chain B from PDB  Type:PROTEIN  Length:278
                                                                                                                                                                                                                                                                                                                       
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........ee......eeeeee....hhhhhheee..ee..hhhhhhhhhhhhhhhhh........eeeeeeeee............eeeeeeeeee..eeeeeeeee.....eeeeeeeeeeee..............eeehhhhhhhhhhhhheee.hhhh.eeeeeee..eeeeeee..hhhhhh....hhhhhhhhhhhhhhhh..........eeeeeeeeeee......eeeeeeeee......eeeeeeee.....eeeeeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                5il6 B 4369 VEHLHPLLHRNVSDLRGLRYLSRFSGDESVLAEHRVNGQAVLAGAAMIVMIQAALTDALGGAVPAGRGLVISDLSWRQPFSVDAANNGELFLELSMPAAGDYRIGIYAYDQAAQLQLHCQARASTAEVQAAWLDFSSLGAQVVDVEACYQRFAAMGIEYGAGHRRLLSLVRQGDQALARIALQDPALNSGFALHPALLDAAMQGVMALLLDELEERPALLLPAGLGQCVLLADCPASLQVQIRRAPSTAPDYCFDLALFDDQGQCCAILNQLSFQPLT 4646
                                  4378      4388      4398      4408      4418      4428      4438      4448      4458      4468      4478      4488      4498      4508      4518      4528      4538      4548      4558      4568      4578      4588      4598      4608      4618      4628      4638
   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 5IL6)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5IL6)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5IL6)

(-) Gene Ontology  (10, 10)

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 5il6)
 
  Sites
(no "Sites" information available for 5il6)
 
  Cis Peptide Bonds
    Ala A:4617 - Pro A:4618   [ RasMol ]  
    Ala B:4617 - Pro B:4618   [ 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
  5il6
    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
  Q4KCD8_PSEF5 | Q4KCD8
    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
  Q4KCD8_PSEF5 | Q4KCD8
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

(no "Entries Sharing at Least One Protein Chain" available for 5IL6)

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 5IL6)