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(-) Description

Title :  CRYSTAL STRUCTURE OF HUMAN FPPS IN COMPLEX WITH BIARYL COMPOUND 6
 
Authors :  J. M. Rondeau, E. Bourgier, S. Lehmann
Date :  02 Sep 15  (Deposition) - 30 Sep 15  (Release) - 04 Nov 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.40
Chains :  Asym. Unit :  F
Biol. Unit 1:  F  (2x)
Keywords :  Transferase, Isoprene Biosynthesis, Cholesterol Biosynthesis (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. L. Marzinzik, R. Amstutz, G. Bold, E. Bourgier, S. Cotesta, J. F. Glickman, M. Gotte, C. Henry, S. Lehmann, J. C. Hartwieg, S. Ofner X. Pelle, T. P. Roddy, J. M. Rondeau, F. Stauffer, S. J. Stout, A. Widmer J. Zimmermann, T. Zoller, W. Jahnke
Discovery Of Novel Allosteric Non-Bisphosphonate Inhibitors Of Farnesyl Pyrophosphate Synthase By Integrated Lead Finding.
Chemmedchem V. 10 1884 2015
PubMed-ID: 26381451  |  Reference-DOI: 10.1002/CMDC.201500338
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - FARNESYL PYROPHOSPHATE SYNTHASE
    Chains: F
    EC Number: 2.5.1.10, 2.5.1.1
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PET28
    Expression System Taxid: 469008
    Expression System Variant: TUNER
    Expression System Vector Type: PLASMID
    Fragment: RESIDUES 6-253
    Gene: FDPS, FPS, KIAA1293
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: FPS,(2E,6E)-FARNESYL DIPHOSPHATE SYNTHASE, DIMETHYLALLYLTRANSTRANSFERASE,FARNESYL DIPHOSPHATE SYNTHASE, GERANYLTRANSTRANSFERASE

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : F
Biological Unit 1 (2x): F

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 4)

Asymmetric Unit (3, 4)
No.NameCountTypeFull Name
15BK1Ligand/Ion1H,1'H-4,4'-BIINDOLE-2-CARBOXYLIC ACID
2GOL2Ligand/IonGLYCEROL
3PO41Ligand/IonPHOSPHATE ION
Biological Unit 1 (3, 8)
No.NameCountTypeFull Name
15BK2Ligand/Ion1H,1'H-4,4'-BIINDOLE-2-CARBOXYLIC ACID
2GOL4Ligand/IonGLYCEROL
3PO42Ligand/IonPHOSPHATE ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG F:141 , GLU F:158 , LEU F:161 , HOH F:501 , HOH F:519 , HOH F:526binding site for residue GOL F 401
2AC2SOFTWARETYR F:119 , GLN F:120 , GLY F:125 , HOH F:509binding site for residue GOL F 402
3AC3SOFTWARETYR F:10 , LYS F:57 , ASN F:59 , ARG F:60 , THR F:63 , SER F:205 , PHE F:206 , PHE F:239 , LEU F:344 , LYS F:347 , PO4 F:404 , HOH F:550binding site for residue 5BK F 403
4AC4SOFTWAREGLY F:56 , LYS F:57 , GLN F:96 , ARG F:113 , 5BK F:403 , HOH F:516 , HOH F:517 , HOH F:521 , HOH F:550binding site for residue PO4 F 404

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Ala F:334 -Pro F:335

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5DJR)

(-) 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 F from PDB  Type:PROTEIN  Length:342
                                                                                                                                                                                                                                                                                                                                                                                      
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...ee..ee.hhhh..hhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhh..........hhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...........hhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5djr F   9 VYAQEKQDFVQHFSQIVRVLTEDEMGHPEIGDAIARLKEVLEYNAIGGKYNRGLTVVVAFRELVEPRKQDADSLQRAWTVGWCVELLQAFFLVADDIMDSSLTRRGQICWYQKPGVGLDAINDANLLEACIYRLLKLYCREQPYYLNLIELFLQSSYQTEIGQTLDLLTAPQGNVDLVRFTEKRYKSIVKYKTAFYSFYLPIAAAMYMAGIDGEKEHANAKKILLEMGEFFQIQDDYLDLFGDPSVTGKIGTDIQDNKCSWLVVQCLQRATPEQYQILKENYGQKEAEKVARVKALYEELDLPAVFLQYEEDSYSHIMALIEQYAAPLPPAVFLGLARKIYK 350
                                    18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348
   Legend:   → Mismatch (orange background)
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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  (0, 0)

(no "SCOP Domain" information available for 5DJR)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (17, 17)

Asymmetric Unit(hide GO term definitions)

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  Cis Peptide Bonds
    Ala F:334 - Pro F:335   [ RasMol ]  
 
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  FPPS_HUMAN | P14324
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 Related Entries

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

UniProtKB/Swiss-Prot
        FPPS_HUMAN | P14324: 1yq7 1yv5 1zw5 2f7m 2f89 2f8c 2f8z 2f92 2f94 2f9k 2opm 2opn 2qis 2rah 2vf6 3b7l 3cp6 3n1v 3n1w 3n3l 3n45 3n46 3n49 3n5h 3n5j 3n6k 3rye 3s4j 4dem 4ga3 4h5c 4h5d 4h5e 4jvj 4kfa 4kpd 4kpj 4kq5 4kqs 4kqu 4l2x 4lfv 4lpg 4lph 4n1z 4n9u 4nfi 4nfj 4nfk 4ng6 4nke 4nkf 4nua 4ogu 4p0v 4p0w 4p0x 4pvx 4pvy 4q23 4qpf 4qxs 4rxa 4xqr 4xqs 4xqt 5cg5 5cg6 5dgm 5dgn 5dgs 5diq 5djp 5djv 5ja0 5juz 5jv0 5jv1 5jv2 5ksx

(-) Related Entries Specified in the PDB File

5dgn HUMAN FPPS COMPLEX WITH BIARYL COMPOUND 8A
5diq HUMAN FPPS COMPLEX WITH SALICYLIC ACID DERIVATIVE 3A
5djp HUMAN FPPS COMPLEX WITH BIARYL COMPOUND 5