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(-) Description

Title :  BINDING AND STRUCTURAL STUDIES OF A 5,5-DIFLUOROMETHYL ADENOSINE NUCLEOSIDE WITH THE FLUORINASE ENZYME
 
Authors :  S. Thompson, S. A. Mcmahon, J. H. Naismith, D. O'Hagan
Date :  02 Oct 15  (Deposition) - 23 Dec 15  (Release) - 23 Dec 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.84
Chains :  Asym. Unit :  A,B,C
Biol. Unit 1:  A,B,C  (2x)
Keywords :  Transferase, Fluorinase, Difluoromethyl, Isothermal Titration Calorimetry, (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. Thompson, S. A. Mcmahon, J. H. Naismith, D. O'Hagan
Exploration Of A Potential Difluoromethyl-Nucleoside Substrate With The Fluorinase Enzyme.
Bioorg. Chem. V. 64 37 2015
PubMed-ID: 26642178  |  Reference-DOI: 10.1016/J.BIOORG.2015.11.003

(-) Compounds

Molecule 1 - 5'-FLUORO-5'-DEOXY-ADENOSINE SYNTHASE
    Chains: A, B, C
    EC Number: 2.5.1.63
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector: PET
    Expression System Vector Type: PLASMID
    Organism Scientific: STREPTOMYCES CATTLEYA
    Organism Taxid: 29303
    Synonym: 5-FDAS, 5-FLUORODEOXYADENOSINE SYNTHASE, FLUORINASE

 Structural Features

(-) Chains, Units

  123
Asymmetric Unit : ABC
Biological Unit 1 (2x): ABC

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (2, 6)
No.NameCountTypeFull Name
1TLA3Ligand/IonL(+)-TARTARIC ACID
2Y3J3Ligand/Ion5,5-DIFLUOROMETHYL ADENOSINE
Biological Unit 1 (2, 12)
No.NameCountTypeFull Name
1TLA6Ligand/IonL(+)-TARTARIC ACID
2Y3J6Ligand/Ion5,5-DIFLUOROMETHYL ADENOSINE

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:16 , TRP A:50 , THR A:76 , TYR A:77 , PRO A:78 , THR A:80 , THR A:155 , PHE A:156 , TYR A:157 , SER A:158 , PHE C:213 , ASN C:215 , PHE C:254 , ARG C:277 , ALA C:279 , TLA C:1300BINDING SITE FOR RESIDUE Y3J A1299
2AC2SOFTWAREPHE A:213 , ASN A:215 , PHE A:254 , ARG A:277 , ALA A:279 , TLA A:1300 , ASP B:16 , TRP B:50 , THR B:76 , TYR B:77 , PRO B:78 , THR B:80 , THR B:155 , PHE B:156 , TYR B:157 , SER B:158BINDING SITE FOR RESIDUE Y3J B1299
3AC3SOFTWAREPHE B:213 , ASN B:215 , PHE B:254 , ARG B:277 , ALA B:279 , TLA B:1300 , ASP C:16 , TRP C:50 , TYR C:77 , PRO C:78 , THR C:80 , THR C:155 , PHE C:156 , TYR C:157 , SER C:158BINDING SITE FOR RESIDUE Y3J C1299
4AC4SOFTWAREASP A:210 , PHE A:213 , ASN A:215 , TRP A:217 , SER A:269 , ARG A:270 , HOH A:2109 , HOH A:2110 , HOH A:2125 , LEU B:17 , SER B:23 , THR B:155 , Y3J B:1299BINDING SITE FOR RESIDUE TLA A1300
5AC5SOFTWARELEU A:17 , SER A:23 , THR A:155 , Y3J A:1299 , HOH A:2014 , HOH A:2093 , ASP C:210 , PHE C:213 , ASN C:215 , SER C:269 , ARG C:270 , HOH C:2055BINDING SITE FOR RESIDUE TLA C1300
6AC6SOFTWAREASP B:210 , PHE B:213 , ASN B:215 , SER B:269 , ARG B:270 , HOH B:2085 , HOH B:2086 , HOH B:2106 , LEU C:17 , SER C:23 , THR C:155 , Y3J C:1299BINDING SITE FOR RESIDUE TLA B1300

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5FIU)

(-) Cis Peptide Bonds  (3, 3)

Asymmetric Unit
No.Residues
1His A:211 -Pro A:212
2His B:211 -Pro B:212
3His C:211 -Pro C:212

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5FIU)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5FIU)

(-) Exons   (0, 0)

(no "Exon" information available for 5FIU)

(-) 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:291
                                                                                                                                                                                                                                                                                                                                   
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee......hhhhhhhhhhhhhh...eeeeee......hhhhhhhhhh.hhhhh....eeeee...........eeeee..........................eeee.....hhhhhhhhheeeeee..............hhhhhhhhhhhhhhhh..hhhhh....hhhhh........eee..eeeeeeeeee....eeeeeeehhhhhhh......eeeeee.....eeeeee.hhhhhh....eeeee....eeeeee....hhhhhh.....eeeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5fiu A   8 RPIIAFMSDLGTTDDSVAQCKGLMYSICPDVTVVDVCHSMTPWDVEEGARYIVDLPRFFPEGTVFATTTYPATGTTTRSVAVRIKQAAKGGARGQWAGSGAGFERAEGSYIYIAPNNGLLTTVLEEHGYLEAYEVTSPKVIPEQPEPTFYSREMVAIPSAHLAAGFPLSEVGRPLEDHEIVRFNRPAVEQDGEALVGVVSAIDHPFGNVWTNIHRTDLEKAGIGYGARLRLTLDGVLPFEAPLTPTFADAGEIGNIAIYLNSRGYLSIARNAASLAYPYHLKEGMSARVEA 298
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297 


Chain B from PDB  Type:PROTEIN  Length:291
                                                                                                                                                                                                                                                                                                                                   
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee......hhhhhhhhhhhhhh...eeeeee......hhhhhhhhhh.hhhhh....eeeee...........eeeee..........................eeee.....hhhhhhhhheeeeee..............hhhhhhhhhhhhhhhh..hhhhh....hhhhh........eee..eeeeeeeeee....eeeeeeehhhhhhh......eeeeee...eeeeeeee..hhhhh....eeeee....eeeeee....hhhhhh.....eeeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5fiu B   8 RPIIAFMSDLGTTDDSVAQCKGLMYSICPDVTVVDVCHSMTPWDVEEGARYIVDLPRFFPEGTVFATTTYPATGTTTRSVAVRIKQAAKGGARGQWAGSGAGFERAEGSYIYIAPNNGLLTTVLEEHGYLEAYEVTSPKVIPEQPEPTFYSREMVAIPSAHLAAGFPLSEVGRPLEDHEIVRFNRPAVEQDGEALVGVVSAIDHPFGNVWTNIHRTDLEKAGIGYGARLRLTLDGVLPFEAPLTPTFADAGEIGNIAIYLNSRGYLSIARNAASLAYPYHLKEGMSARVEA 298
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297 


Chain C from PDB  Type:PROTEIN  Length:291
                                                                                                                                                                                                                                                                                                                                   
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee......hhhhhhhhhhhhhh...eeeeee......hhhhhhhhhh.hhhhh....eeeee...........eeeee..........................eeee.....hhhhhhhhheeeeee..............hhhhhhhhhhhhhhhh..hhhhh....hhhhh........eee..eeeeeeeeee....eeeeeeehhhhhhh......eeeeee...eeeeeeee.hhhhhh....eeeee....eeeeee...............eeeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5fiu C   8 RPIIAFMSDLGTTDDSVAQCKGLMYSICPDVTVVDVCHSMTPWDVEEGARYIVDLPRFFPEGTVFATTTYPATGTTTRSVAVRIKQAAKGGARGQWAGSGAGFERAEGSYIYIAPNNGLLTTVLEEHGYLEAYEVTSPKVIPEQPEPTFYSREMVAIPSAHLAAGFPLSEVGRPLEDHEIVRFNRPAVEQDGEALVGVVSAIDHPFGNVWTNIHRTDLEKAGIGYGARLRLTLDGVLPFEAPLTPTFADAGEIGNIAIYLNSRGYLSIARNAASLAYPYHLKEGMSARVEA 298
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297
   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 5FIU)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5FIU)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5FIU)

(-) Gene Ontology  (2, 2)

Asymmetric Unit(hide GO term definitions)

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        FLA_STRCT | Q70GK9: 1rqp 1rqr 2c2w 2c4t 2c4u 2c5b 2c5h 2cbx 2cc2 2v7t 2v7u 2v7v 2v7w 2v7x 4cqj

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