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 DEPH
 
Authors :  D. H. Scharf, M. Groll, A. Habel, T. Heinekamp, C. Hertweck, A. A. Brakha E. M. Huber
Date :  02 Dec 13  (Deposition) - 05 Mar 14  (Release) - 05 Mar 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Disulfide Bond, Natural Sulfur Products, Romidepsin, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  D. H. Scharf, M. Groll, A. Habel, T. Heinekamp, C. Hertweck, A. A. Brakhage, E. M. Huber
Flavoenzyme-Catalyzed Formation Of Disulfide Bonds In Natural Products
Angew. Chem. Int. Ed. Engl. V. 53 2221 2014
PubMed-ID: 24446392  |  Reference-DOI: 10.1002/ANIE.201309302

(-) Compounds

Molecule 1 - DEPH
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET43.1
    Expression System Strain: BL21 (DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: DEPH
    Organism Scientific: CHROMOBACTERIUM VIOLACEUM
    Organism Taxid: 536

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 15)

Asymmetric/Biological Unit (3, 15)
No.NameCountTypeFull Name
1CL6Ligand/IonCHLORIDE ION
2FAD2Ligand/IonFLAVIN-ADENINE DINUCLEOTIDE
3NA7Ligand/IonSODIUM ION

(-) Sites  (15, 15)

Asymmetric Unit (15, 15)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREILE A:11 , GLY A:12 , SER A:14 , HIS A:15 , ALA A:16 , ILE A:34 , ASP A:35 , ALA A:36 , GLY A:37 , ALA A:38 , ARG A:40 , ASN A:41 , SER A:47 , HIS A:48 , ASP A:80 , SER A:81 , VAL A:82 , PHE A:111 , ASP A:115 , TRP A:127 , CYS A:137 , HIS A:138 , SER A:231 , GLY A:267 , ASP A:268 , GLY A:274 , THR A:275 , VAL A:276 , NA A:304 , CL A:306 , HOH A:401 , HOH A:402 , HOH A:408 , HOH A:412 , HOH A:418 , HOH A:422 , HOH A:425 , HOH A:427 , HOH A:430BINDING SITE FOR RESIDUE FAD A 301
02AC2SOFTWAREGLY A:267 , ASP A:268 , GLY A:273 , GLY A:274 , THR A:275 , ALA A:279BINDING SITE FOR RESIDUE NA A 302
03AC3SOFTWARESER A:47 , HIS A:48 , GLY A:49 , VAL A:50 , GLN A:53BINDING SITE FOR RESIDUE NA A 303
04AC4SOFTWAREARG A:40 , GLY A:112 , VAL A:113 , ASP A:268 , FAD A:301BINDING SITE FOR RESIDUE NA A 304
05AC5SOFTWAREHIS A:271 , ASP B:204BINDING SITE FOR RESIDUE CL A 305
06AC6SOFTWAREHIS A:133 , CYS A:134 , FAD A:301BINDING SITE FOR RESIDUE CL A 306
07AC7SOFTWARECYS A:239 , ALA A:240 , ARG A:251 , THR A:258 , SER A:259BINDING SITE FOR RESIDUE CL A 307
08AC8SOFTWAREILE B:11 , GLY B:12 , SER B:14 , HIS B:15 , ALA B:16 , ILE B:34 , ASP B:35 , ALA B:36 , GLY B:37 , ALA B:38 , ARG B:40 , ASN B:41 , SER B:47 , HIS B:48 , ASP B:80 , SER B:81 , VAL B:82 , PHE B:111 , ASP B:115 , CYS B:137 , HIS B:138 , SER B:230 , GLY B:267 , ASP B:268 , GLY B:274 , THR B:275 , VAL B:276 , NA B:305 , CL B:307 , HOH B:401 , HOH B:403 , HOH B:410 , HOH B:413 , HOH B:421 , HOH B:426 , HOH B:431 , HOH B:446 , HOH B:578BINDING SITE FOR RESIDUE FAD B 301
09AC9SOFTWAREASP B:268 , GLY B:273 , GLY B:274 , THR B:275 , ALA B:279 , HOH B:584BINDING SITE FOR RESIDUE NA B 302
10BC1SOFTWAREASP B:174 , VAL B:195 , ASP B:197BINDING SITE FOR RESIDUE NA B 303
11BC2SOFTWAREALA B:63 , HOH B:461 , HOH B:481BINDING SITE FOR RESIDUE NA B 304
12BC3SOFTWAREASN B:41 , SER B:47 , FAD B:301 , HOH B:578BINDING SITE FOR RESIDUE NA B 305
13BC4SOFTWAREPHE A:43 , GLU A:124 , MET B:4 , ARG B:103BINDING SITE FOR RESIDUE CL B 306
14BC5SOFTWAREHIS B:133 , CYS B:134 , FAD B:301BINDING SITE FOR RESIDUE CL B 307
15BC6SOFTWAREHOH A:465 , ARG B:29 , HOH B:432BINDING SITE FOR RESIDUE CL B 308

(-) SS Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1A:134 -A:137
2B:134 -B:137

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4NTE)

(-) 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:292
                                                                                                                                                                                                                                                                                                                                    
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeee..hhhhhhhhhhhhhh...eeeee.....................hhhhhhhhhhhhhhh...eeeee..eeeee...eeeee....eeeeeeeee...eeee......hhhhh...ee.hhhhhhhhhheeeeeee..hhhhhhhhhhh...eeeeee.......hhhhhhhhhhh..eee...eeeee..eeeee....eeee.eeee..eeee..hhhhhh...eee....eee............eee.hhhh....hhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4nte A   4 MLFDVIVIGGSHAGQSAALQIARARRRVLVIDAGARRNRFASQSHGVIGQDGRSPDAIAADGKAQLLAYPNAQWREDSVVRAERSGYTLICASGQHYRACQLVLAFGVVDELPELEGLEERWGESVFHCPYCHGYELDGGRIGVLGSGPLSYLSAMLMPEWGQTVFLTDASFEPDEEQREALARRGVEIVRDRIARIVDRATVELADGRRIAFDGLFTMNRMRLSSPVAEQLGCAIEEGPLGPYVRTDDAMETSTPGVFACGDITHRGGTVALAIGNGALAGIAAHRKLVFG 297
                                    13        23        33        43        53        63        73        83    ||  95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295  
                                                                                                               88|                                                                                                                                                                                                              
                                                                                                                91                                                                                                                                                                                                              


Chain B from PDB  Type:PROTEIN  Length:296
                                                                                                                                                                                                                                                                                                                                        
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeeee..hhhhhhhhhhhhhh...eeeee.....................hhhhhhhhhhhhhhh...eeeee..eeeeee...eeeee....eeeeeeeee...eeee......hhhhh...ee.hhhhhhhhhh..eeeee..hhhhhhhhhhhhhh.eeeee........hhhhhhhhhh..eee...eeeee...eeee....eee..eeee..eeee..hhhhhh...eeee..eeee............eee.hhhh....hhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4nte B   1 TSPMLFDVIVIGGSHAGQSAALQIARARRRVLVIDAGARRNRFASQSHGVIGQDGRSPDAIAADGKAQLLAYPNAQWREDSVVRAERSDGYTLICASGQHYRACQLVLAFGVVDELPELEGLEERWGESVFHCPYCHGYELDGGRIGVLGSGPLSYLSAMLMPEWGQTVFLTDASFEPDEEQREALARRGVEIVRDRIARIVDRATVELADGRRIAFDGLFTMNRMRLSSPVAEQLGCAIEEGPLGPYVRTDDAMETSTPGVFACGDITHRGGTVALAIGNGALAGIAAHRKLVFG 297
                                    10        20        30        40        50        60        70        80        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291      
                                                                                                                   89|                                                                                                                                                                                                              
                                                                                                                    91
   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 4NTE)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (3, 3)

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
    CL  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    FAD  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    NA  [ 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 ]
    AC9  [ RasMol ]  +environment [ RasMol ]
    BC1  [ RasMol ]  +environment [ RasMol ]
    BC2  [ RasMol ]  +environment [ RasMol ]
    BC3  [ RasMol ]  +environment [ RasMol ]
    BC4  [ RasMol ]  +environment [ RasMol ]
    BC5  [ RasMol ]  +environment [ RasMol ]
    BC6  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 4nte)
 

(-) 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
  4nte
    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
  A4ZPY8_CHRVL | A4ZPY8
    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
  A4ZPY8_CHRVL | A4ZPY8
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/TrEMBL
        A4ZPY8_CHRVL | A4ZPY8: 4jn9 4jna

(-) Related Entries Specified in the PDB File

4ntc
4ntd OXIDOREDUCTASE HLMI FROM STREPTOMYCES CLAVULIGERUS