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 DYP-TYPE PEROXIDASE FROM THERMOBIFIDA CELLULOSILYTICA
 
Authors :  T. Lukk, A. M. A. Hetta, A. Jones, J. Solbiati, S. Majumdar, J. E. Cronan, J. A. Gerlt, S. K. Nair
Date :  27 Aug 12  (Deposition) - 11 Sep 13  (Release) - 11 Sep 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.70
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Ferridoxin-Like, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  T. Lukk, A. M. A. Hetta, A. Jones, J. Solbiati, S. Majumdar, J. E. Cronan J. A. Gerlt, S. K. Nair
Dyp-Type Peroxidases From Stretptomyces And Thermobifida Ca Modify Organosolv Lignin.
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - DYP-TYPE PEROXIDASE
    Chains: A, B
    EC Number: 1.11.1.19
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET15B
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Organism Scientific: THERMOBIFIDA CELLULOSILYTICA
    Organism Taxid: 144786

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 7)

Asymmetric/Biological Unit (3, 7)
No.NameCountTypeFull Name
1GOL3Ligand/IonGLYCEROL
2HEM2Ligand/IonPROTOPORPHYRIN IX CONTAINING FE
3OXY2Ligand/IonOXYGEN MOLECULE

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASN A:234 , GLN A:238 , ILE A:239 , GLY A:241 , THR A:242 , ALA A:243 , ILE A:280 , HIS A:336 , ALA A:340 , PRO A:342 , ARG A:352 , PHE A:373 , PHE A:384 , GLN A:388 , LEU A:398 , THR A:402 , HIS A:404 , OXY A:502 , HOH A:612 , HOH A:649 , HOH A:771 , HOH A:797BINDING SITE FOR RESIDUE HEM A 501
2AC2SOFTWAREASP A:240 , ARG A:352 , HEM A:501 , HOH A:1027BINDING SITE FOR RESIDUE OXY A 502
3AC3SOFTWAREASP A:164 , LEU A:165 , GLY A:179 , ALA A:408 , LEU A:409 , HOH A:608 , HOH A:676 , HOH A:718BINDING SITE FOR RESIDUE GOL A 503
4AC4SOFTWAREASN B:234 , GLN B:238 , ILE B:239 , GLY B:241 , THR B:242 , ALA B:243 , ILE B:280 , HIS B:336 , VAL B:337 , ALA B:340 , PRO B:342 , ARG B:352 , PHE B:373 , PHE B:384 , GLN B:388 , LEU B:398 , THR B:402 , OXY B:502 , HOH B:613 , HOH B:650 , HOH B:662 , HOH B:669BINDING SITE FOR RESIDUE HEM B 501
5AC5SOFTWAREASP B:240 , ARG B:352 , HEM B:501 , HOH B:983BINDING SITE FOR RESIDUE OXY B 502
6AC6SOFTWAREASP B:164 , LEU B:165 , GLY B:179 , ALA B:408 , LEU B:409 , HOH B:624 , HOH B:663 , HOH B:825BINDING SITE FOR RESIDUE GOL B 503
7AC7SOFTWAREGLU A:359 , GLY A:360 , HOH A:1017 , HIS B:85 , SER B:214 , LEU B:215 , ARG B:216 , GLU B:359 , HOH B:671BINDING SITE FOR RESIDUE GOL B 504

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4GS1)

(-) Cis Peptide Bonds  (5, 5)

Asymmetric/Biological Unit
No.Residues
1Ala A:71 -Pro A:72
2Ala A:206 -Pro A:207
3Ala B:71 -Pro B:72
4Glu B:93 -Pro B:94
5Ala B:206 -Pro B:207

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4GS1)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4GS1)

(-) Exons   (0, 0)

(no "Exon" information available for 4GS1)

(-) 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:375
                                                                                                                                                                                                                                                                                                                                                                                                                       
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhh..................eeeeeeeeehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhh.......eeeeeehhhhhhhh.hhhhhhhhhh..........hhhhh...eeeeeee.hhhhhhhhhhhhhhhhh..eeeeeeeeee..hhhhh.......................hhhhhhhhh.....hhhhhhhh..eeeeeeeeeehhhhhh..hhhhhhhhhh..................................hhhhhhhhhhh.....ee..eeeeeee.....eeeeeeeeeee.hhhhhhhhhhhhhhhh...hhh.eeeeeeeeeee.........hhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4gs1 A  53 PVDAQRLDMARRRADANAAPQPGISGRAPAFVHVIAFDLAEPARAEPAAAREGAATALRTWAEHAARLHADGPEGAASAGLLPASLMVTIGIGGSLLEAMDAADRRPDALADLPEFATDDLRPRWCGGDLMLQVGAEDPMVLAAAVDELVAATAPTTTVRWSLRGFRRTAAAAQDPDATPRNLMGQIDGTANPAQDHPLFTRTVTAPPADDPAHAWMDGGSYLVVRRIRMLLDEWRRLDVPDRERVIGRHLDTGAPLGGEKETDPVVLTARDADGRLVIPEDAHVRLANPENNLGARMVRRGYNYDEGWRDDGVRDAGLLFMAWQGNPATGFVPVQRSLVEQGDALNRYTRHEGSALFAVPAATADRYPGQDLVE 427
                                    62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402       412       422     


Chain B from PDB  Type:PROTEIN  Length:376
                                                                                                                                                                                                                                                                                                                                                                                                                        
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhh..................eeeeeeeee..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..............eeeeeehhhhhhhh.hhhhhhhhhh..........hhhhh...eeeeeee.hhhhhhhhhhhhhhhhh..eeeeeeeeee..hhhhh.......................hhhhhhhhh.....hhhhhhhh..eeeeeeeeeehhhhhhhhhhhhhhhhhh..................................hhhhhhhhhhh.....ee..eeeeeee.....eeeeeeeeeee.hhhhhhhhhhhhhhhh.hhhhh.eeeeeeeeeee.........hhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4gs1 B  53 PVDAQRLDMARRRADANAAPQPGISGRAPAFVHVIAFDLAEPARAEPAAAREGAATALRTWAEHAARLHADGPEGAASAGLLPASLMVTIGIGGSLLEAMDAADRRPDALADLPEFATDDLRPRWCGGDLMLQVGAEDPMVLAAAVDELVAATAPTTTVRWSLRGFRRTAAAAQDPDATPRNLMGQIDGTANPAQDHPLFTRTVTAPPADDPAHAWMDGGSYLVVRRIRMLLDEWRRLDVPDRERVIGRHLDTGAPLGGEKETDPVVLTARDADGRLVIPEDAHVRLANPENNLGARMVRRGYNYDEGWRDDGVRDAGLLFMAWQGNPATGFVPVQRSLVEQGDALNRYTRHEGSALFAVPAATADRYPGQDLVEG 428
                                    62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402       412       422
   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 4GS1)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4GS1)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4GS1)

(-) Gene Ontology  (5, 5)

Asymmetric/Biological Unit(hide GO term definitions)

 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
    GOL  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    HEM  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    OXY  [ 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 ]
 
  Cis Peptide Bonds
    Ala A:206 - Pro A:207   [ RasMol ]  
    Ala A:71 - Pro A:72   [ RasMol ]  
    Ala B:206 - Pro B:207   [ RasMol ]  
    Ala B:71 - Pro B:72   [ RasMol ]  
    Glu B:93 - Pro B:94   [ 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
  4gs1
    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
  U3KRF5_9ACTN | U3KRF5
    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)
  1.11.1.19
    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
  U3KRF5_9ACTN | U3KRF5
    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 4GS1)

(-) Related Entries Specified in the PDB File

4grc 4gt2 4gu7