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(-) Description

Title :  COMPLEXES OF DODECIN WITH FLAVIN AND FLAVIN-LIKE LIGANDS
 
Authors :  M. Grininger, K. Zeth, D. Oesterhelt
Date :  12 Jan 06  (Deposition) - 15 Feb 06  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.27
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (12x)
Keywords :  Flavoprotein, Flavin, Flavin-Like Ligands (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. Grininger, K. Zeth, D. Oesterhelt
Dodecins: A Family Of Lumichrome Binding Proteins.
J. Mol. Biol. V. 357 842 2006
PubMed-ID: 16460756  |  Reference-DOI: 10.1016/J.JMB.2005.12.072

(-) Compounds

Molecule 1 - VNG1446H
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET22B
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Organism Scientific: HALOBACTERIUM SALINARUM
    Organism Taxid: 478009
    Other Details: LUMICHROME BOUND
    Other Details - Source: GERMAN COLLECTION OF MICROORGANISMS (DSM 671)
    Strain: R1
    Synonym: DODECIN

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 6)

Asymmetric Unit (5, 6)
No.NameCountTypeFull Name
1CL1Ligand/IonCHLORIDE ION
2LUM1Ligand/IonLUMICHROME
3MG2Ligand/IonMAGNESIUM ION
4NA1Ligand/IonSODIUM ION
5SO41Ligand/IonSULFATE ION
Biological Unit 1 (2, 24)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2LUM12Ligand/IonLUMICHROME
3MG-1Ligand/IonMAGNESIUM ION
4NA-1Ligand/IonSODIUM ION
5SO412Ligand/IonSULFATE ION

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:41 , HOH A:2048 , HOH A:2049 , HOH A:2050 , HOH A:2051 , HOH A:2071BINDING SITE FOR RESIDUE MG A 102
2AC2SOFTWARECL A:105 , HOH A:2008 , HOH A:2072BINDING SITE FOR RESIDUE NA A 104
3AC3SOFTWAREGLN A:59 , NA A:104BINDING SITE FOR RESIDUE CL A 105
4AC4SOFTWAREGLU A:14 , GLU A:51 , HOH A:2020 , HOH A:2026 , HOH A:2027 , HOH A:2033 , HOH A:2063BINDING SITE FOR RESIDUE MG A1066
5AC5SOFTWARESER A:15 , PHE A:16 , THR A:17 , HOH A:2082 , HOH A:2083 , HOH A:2084 , HOH A:2085BINDING SITE FOR RESIDUE SO4 A1067
6AC6SOFTWARETRP A:36 , VAL A:44 , GLU A:45 , GLN A:55 , HOH A:2048 , HOH A:2057BINDING SITE FOR RESIDUE LUM A1068

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2CC6)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2CC6)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2CC6)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2CC6)

(-) Exons   (0, 0)

(no "Exon" information available for 2CC6)

(-) 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 d2cc6a_ A: automated matches                                     SCOP domains
               CATH domains 2cc6A00 A:2-65 Flavin-binding protein dodecin                    CATH domains
               Pfam domains ---------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeeeee..hhhhhhhhhhhhhhhhh..eeeeeeeeeeee.......eeeeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------- Transcript
                  2cc6 A  2 VFKKVLLTGTSEESFTAAADDAIDRAEDTLDNVVWAEVVDQGVEIGAVEERTYQTEVQVAFELD 65
                                    11        21        31        41        51        61    


Chain A from PDB  Type:PROTEIN  Length:64
 aligned with Q9HPW4_HALSA | Q9HPW4 from UniProtKB/TrEMBL  Length:77

    Alignment length:64
                                    20        30        40        50        60        70    
          Q9HPW4_HALSA   11 VFKKVLLTGTSEESFTAAADDAIDRAEDTLDNVVWAEVVDQGVEIGAVEERTYQTEVQVAFELD 74
               SCOP domains d2cc6a_ A: automated matches                                     SCOP domains
               CATH domains 2cc6A00 A:2-65 Flavin-binding protein dodecin                    CATH domains
               Pfam domains ---------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeeeee..hhhhhhhhhhhhhhhhh..eeeeeeeeeeee.......eeeeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------- Transcript
                  2cc6 A  2 VFKKVLLTGTSEESFTAAADDAIDRAEDTLDNVVWAEVVDQGVEIGAVEERTYQTEVQVAFELD 65
                                    11        21        31        41        51        61
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
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  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  (1, 1)

Asymmetric Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2CC6)

(-) Gene Ontology  (3, 3)

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.

Chain A   (Q9HPW4_HALSA | Q9HPW4)
molecular function
    GO:0000166    nucleotide binding    Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.

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  2cc6
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  Q9HPW4_HALSA | Q9HPW4
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 Related Entries

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

UniProtKB/Swiss-Prot
        DODEC_HALS3 | B0R5M0: 1mog 2cc7 2cc8 2cc9 2ccb 2ccc 2cie 2cif 2cjc 2vkf 2vkg 2vx9 4b2h 4b2j 4b2k 4b2m
        Q9HPW4_HALSA | Q9HPW4: 2cc8 2ccb
UniProtKB/TrEMBL
        Q9HPW4_HALSA | Q9HPW4: 1mog 2cc7 2cc9 2ccc 2cie 2cif 2cjc 2vkf 2vkg

(-) Related Entries Specified in the PDB File

1mog CRYSTAL STRUCTURE OF H. SALINARUM DODECIN
2cc7 COMPLEXES OF DODECIN WITH FLAVIN AND FLAVIN -LIKE LIGANDS
2cc8 COMPLEXES OF DODECIN WITH FLAVIN AND FLAVIN -LIKE LIGANDS
2cc9 COMPLEXES OF DODECIN WITH FLAVIN AND FLAVIN -LIKE LIGANDS
2ccb COMPLEXES OF DODECIN WITH FLAVIN AND FLAVIN -LIKE LIGANDS
2ccc COMPLEXES OF DODECIN WITH FLAVIN AND FLAVIN -LIKE LIGANDS