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
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)

(-) Description

Title :  COMPLEXES OF DODECIN WITH FLAVIN AND FLAVIN-LIKE LIGANDS
 
Authors :  H. Staudt, M. Hoesl, A. Dreuw, S. Serdjukow, D. Oesterhelt, N. Budisa, J. Wachtveitl, M. Grininger
Date :  16 Jul 12  (Deposition) - 29 May 13  (Release) - 29 May 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (12x)
Keywords :  Flavoprotein, Incorporation Of Artificial (Non-Canonical) Amino Acids, Protein Reaction Control (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Y. Yu, B. Heidel, T. L. Parapugna, S. Wenderhold-Reeb, B. Song, H. Schonherr, M. Grininger, G. Noll
The Flavoprotein Dodecin As A Redox Probe For Electron Transfer Through Dna.
Angew. Chem. Int. Ed. Engl. V. 52 4950 2013
PubMed-ID: 23532984  |  Reference-DOI: 10.1002/ANIE.201208987

(-) Compounds

Molecule 1 - DODECIN
    Atcc: 49980
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PQE80L
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Organism Scientific: HALOBACTERIUM SALINARUM
    Organism Taxid: 478009
    Other Details: TRYPTOPHAN 36 EXCHANGED BY 4AZATRYPTOPHAN, RIBOFLAVIN BOUND
    Other Details - Source: GERMAN COLLECTION OF MICROORGANISMS (DSM 671)
    Strain: R1

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (12x): A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (6, 7)

Asymmetric Unit (6, 7)
No.NameCountTypeFull Name
14AW1Mod. Amino Acid4-AZATRYPTOPHAN
2CL1Ligand/IonCHLORIDE ION
3MG2Ligand/IonMAGNESIUM ION
4NA1Ligand/IonSODIUM ION
5RBF1Ligand/IonRIBOFLAVIN
6SO41Ligand/IonSULFATE ION
Biological Unit 1 (3, 36)
No.NameCountTypeFull Name
14AW12Mod. Amino Acid4-AZATRYPTOPHAN
2CL-1Ligand/IonCHLORIDE ION
3MG-1Ligand/IonMAGNESIUM ION
4NA-1Ligand/IonSODIUM ION
5RBF12Ligand/IonRIBOFLAVIN
6SO412Ligand/IonSULFATE ION

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLU A:14 , GLU A:51 , HOH A:2023 , HOH A:2024 , HOH A:2028 , HOH A:2029BINDING SITE FOR RESIDUE MG A 101
2AC2SOFTWAREASP A:41 , HOH A:2065BINDING SITE FOR RESIDUE MG A 102
3AC3SOFTWARECL A:104 , HOH A:2066 , HOH A:2067BINDING SITE FOR RESIDUE NA A 103
4AC4SOFTWAREGLN A:59 , NA A:103 , HOH A:2036BINDING SITE FOR RESIDUE CL A 104
5AC5SOFTWARESER A:15 , PHE A:16 , THR A:17 , HOH A:2068BINDING SITE FOR RESIDUE SO4 A 300
6AC6SOFTWARE4AW A:36 , VAL A:44 , GLU A:45 , GLN A:55 , HOH A:2049 , HOH A:2069BINDING SITE FOR RESIDUE RBF A1067

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4B2M)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4B2M)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4B2M)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4B2M)

(-) Exons   (0, 0)

(no "Exon" information available for 4B2M)

(-) 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:64
 aligned with DODEC_HALS3 | B0R5M0 from UniProtKB/Swiss-Prot  Length:68

    Alignment length:64
                                    11        21        31        41        51        61    
           DODEC_HALS3    2 VFKKVLLTGTSEESFTAAADDAIDRAEDTLDNVVWAEVVDQGVEIGAVEERTYQTEVQVAFELD 65
               SCOP domains d4b2ma_ A: automated matches                                     SCOP domains
               CATH domains ---------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeeeee..hhhhhhhhhhhhhhhhh......eeeeeeee.......eeeeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------- Transcript
                  4b2m A  2 VFKKVLLTGTSEESFTAAADDAIDRAEDTLDNVVwAEVVDQGVEIGAVEERTYQTEVQVAFELD 65
                                    11        21        31    |   41        51        61    
                                                             36-4AW
   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  (1, 1)

Asymmetric Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4B2M)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4B2M)

(-) Gene Ontology  (2, 2)

Asymmetric Unit(hide GO term definitions)
Chain A   (DODEC_HALS3 | B0R5M0)
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.

 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
    4AW  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    CL  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    MG  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    NA  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    RBF  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    SO4  [ 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 4b2m)
 
Biological Unit
  Complete Structure
    Biological Unit 1  [ 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 ](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
  4b2m
    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
  DODEC_HALS3 | B0R5M0
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
 
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
  DODEC_HALS3 | B0R5M0
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        DODEC_HALS3 | B0R5M0: 1mog 2cc6 2cc7 2cc8 2cc9 2ccb 2ccc 2cie 2cif 2cjc 2vkf 2vkg 2vx9 4b2h 4b2j 4b2k

(-) Related Entries Specified in the PDB File

2cc8 COMPLEXES OF DODECIN WITH FLAVIN AND FLAVIN-LIKE LIGANDS
2ccb COMPLEXES OF DODECIN WITH FLAVIN AND FLAVIN-LIKE LIGANDS
2vx9 H. SALINARUM DODECIN E45A MUTANT
4b2h COMPLEXES OF DODECIN WITH FLAVIN AND FLAVIN-LIKE LIGANDS
4b2j COMPLEXES OF DODECIN WITH FLAVIN AND FLAVIN-LIKE LIGANDS
4b2k COMPLEXES OF DODECIN WITH FLAVIN AND FLAVIN-LIKE LIGANDS