Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asymmetric Unit
(-)Asym. Unit - sites
(-)Biological Unit 1
(-)Biol. Unit 1 - sites
(-)Biological Unit 2
(-)Biological Unit 3
(-)Biological Unit 4
collapse expand < >
Image Asymmetric Unit
Asymmetric Unit  (Jmol Viewer)
Image Asym. Unit - sites
Asym. Unit - sites  (Jmol Viewer)
Image Biological Unit 1
Biological Unit 1  (Jmol Viewer)
Image Biol. Unit 1 - sites
Biol. Unit 1 - sites  (Jmol Viewer)
Image Biological Unit 2
Biological Unit 2  (Jmol Viewer)
Image Biological Unit 3
Biological Unit 3  (Jmol Viewer)
Image Biological Unit 4
Biological Unit 4  (Jmol Viewer)

(-) Description

Title :  STRUCTURE OF THE DIOXYGENASE DOMAIN OF SACTE_2871, A NOVEL DIOXYGENASE CARBOHYDRATE-BINDING PROTEIN FUSION FROM THE CELLULOLYTIC BACTERIUM STREPTOMYCES SP. SIREXAA-E
 
Authors :  C. M. Bianchetti, T. E. Takasuka, L. F. Bergeman, C. H. Harmann, B. G. Fox
Date :  31 Dec 12  (Deposition) - 15 May 13  (Release) - 10 Jul 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.55
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  C  (1x)
Biol. Unit 4:  D  (1x)
Keywords :  Iron Center, Intradiol Dioxygenase, Carbohydrate Binding Domain, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  C. M. Bianchetti, C. H. Harmann, T. E. Takasuka, G. L. Hura, K. Dyer, B. G. Fox
Fusion Of Dioxygenase And Lignin-Binding Domains In A Novel Secreted Enzyme From Cellulolytic Streptomyces Sp. Sirexaa-E.
J. Biol. Chem. V. 288 18574 2013
PubMed-ID: 23653358  |  Reference-DOI: 10.1074/JBC.M113.475848

(-) Compounds

Molecule 1 - INTRADIOL RING-CLEAVAGE DIOXYGENASE
    Chains: A, B, C, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PVP68K
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: SACTE_2871
    Organism Scientific: STREPTOMYCES SP. SIREXAA-E
    Organism Taxid: 862751

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): A   
Biological Unit 2 (1x):  B  
Biological Unit 3 (1x):   C 
Biological Unit 4 (1x):    D

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 6)

Asymmetric Unit (2, 6)
No.NameCountTypeFull Name
1CL2Ligand/IonCHLORIDE ION
2FE4Ligand/IonFE (III) ION
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2FE-1Ligand/IonFE (III) ION
Biological Unit 2 (0, 0)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2FE-1Ligand/IonFE (III) ION
Biological Unit 3 (0, 0)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2FE-1Ligand/IonFE (III) ION
Biological Unit 4 (0, 0)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2FE-1Ligand/IonFE (III) ION

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETYR A:138 , HIS A:173 , HIS A:175 , HOH A:449BINDING SITE FOR RESIDUE FE A 301
2AC2SOFTWAREGLY A:194 , ASN A:198BINDING SITE FOR RESIDUE CL A 302
3AC3SOFTWARETYR B:138 , HIS B:173 , HIS B:175 , HOH B:423BINDING SITE FOR RESIDUE FE B 301
4AC4SOFTWARETYR C:138 , HIS C:173 , HIS C:175 , HOH C:445BINDING SITE FOR RESIDUE FE C 301
5AC5SOFTWARETYR D:138 , HIS D:173 , HIS D:175BINDING SITE FOR RESIDUE FE D 301
6AC6SOFTWAREGLY D:194 , ASN D:198BINDING SITE FOR RESIDUE CL D 302

(-) SS Bonds  (2, 2)

Asymmetric Unit
No.Residues
1A:119 -D:119
2B:119 -C:119

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4ILT)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4ILT)

(-) 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:154
                                                                                                                                                                                          
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..............................eeeeeeeeehhhhh.....eeeee...............eeeee.....eeeeeee..........eeeeeee......eeeeee...hhhhh.....hhhhh.eee.....eeee..ee.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ilt A  77 DPTPDQMEGPYFKPDSPPRTSLVTSSTPGVPLTVSGYVFGRACKPLTGVLLDFWQADTGGAYDMTGFAFRGHQFTGADGSFTLRTIVPGLYPGRTRHIHVKAQAPGRPVLTTQLYFPGEPRNTTDALFDPALLMNVRSAGPGREGTFDFVLDVA 230
                                    86        96       106       116       126       136       146       156       166       176       186       196       206       216       226    


Chain B from PDB  Type:PROTEIN  Length:154
                                                                                                                                                                                          
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..............................eeeeeeeeehhhhh.....eeeee...............eeeee.....eeeeeee..........eeeeeee.....eeeeeee...hhhhh.....hhhhh.eee.....eeee..ee.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ilt B  77 DPTPDQMEGPYFKPDSPPRTSLVTSSTPGVPLTVSGYVFGRACKPLTGVLLDFWQADTGGAYDMTGFAFRGHQFTGADGSFTLRTIVPGLYPGRTRHIHVKAQAPGRPVLTTQLYFPGEPRNTTDALFDPALLMNVRSAGPGREGTFDFVLDVA 230
                                    86        96       106       116       126       136       146       156       166       176       186       196       206       216       226    


Chain C from PDB  Type:PROTEIN  Length:155
                                                                                                                                                                                           
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...............................eeeeeeeeehhhhh.....eeeee...............eeeee.....eeeeeee..........eeeeeee.....eeeeeee...hhhhh.....hhhhh.eee.....eeee..ee.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ilt C  76 SDPTPDQMEGPYFKPDSPPRTSLVTSSTPGVPLTVSGYVFGRACKPLTGVLLDFWQADTGGAYDMTGFAFRGHQFTGADGSFTLRTIVPGLYPGRTRHIHVKAQAPGRPVLTTQLYFPGEPRNTTDALFDPALLMNVRSAGPGREGTFDFVLDVA 230
                                    85        95       105       115       125       135       145       155       165       175       185       195       205       215       225     


Chain D from PDB  Type:PROTEIN  Length:154
                                                                                                                                                                                          
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...............................eeeeeeeeehhhhh.....eeeee...............eeeee.....eeeeeee..........eeeeeee.....eeeeeee...hhhhh.....hhhhh.eee.....eeee..ee... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ilt D  76 SDPTPDQMEGPYFKPDSPPRTSLVTSSTPGVPLTVSGYVFGRACKPLTGVLLDFWQADTGGAYDMTGFAFRGHQFTGADGSFTLRTIVPGLYPGRTRHIHVKAQAPGRPVLTTQLYFPGEPRNTTDALFDPALLMNVRSAGPGREGTFDFVLDV 229
                                    85        95       105       115       125       135       145       155       165       175       185       195       205       215       225
   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 4ILT)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (12, 12)

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
    CL  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    FE  [ 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 ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 4ilt)
 
Biological Units
  Complete Structure
    Biological Unit 1  [ Jena3D ]
    Biological Unit 2  [ Jena3D ]
    Biological Unit 3  [ Jena3D ]
    Biological Unit 4  [ 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 | Asym. Unit - sites PNG format | Biol. Unit 1 PNG format | Biol. Unit 1 - sites PNG format | Biol. Unit 2 PNG format | Biol. Unit 3 PNG format | Biol. Unit 4 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
  4ilt
    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
  G2NEL6_STREK | G2NEL6
    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
  G2NEL6_STREK | G2NEL6
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/TrEMBL
        G2NEL6_STREK | G2NEL6: 4ilv

(-) Related Entries Specified in the PDB File

4ilv 4ily 4im1 4im4