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(-) Description

Title :  CRYSTAL STRUCTURE OF HUMAN FPPS IN COMPLEX WITH AN ALLOSTERIC INHIBITOR MIT-01-055
 
Authors :  J. Park, A. Magder, M. Tsakos, Y. S. Tsantrizos, A. M. Berghuis
Date :  10 May 16  (Deposition) - 15 Mar 17  (Release) - 22 Mar 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym. Unit :  F
Biol. Unit 1:  F  (2x)
Keywords :  Transferase, Transferase-Transferase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. Park, C. Y. Leung, A. N. Matralis, C. M. Lacbay, M. Tsakos, G. Fernandez De Troconiz, A. M. Berghuis, Y. S. Tsantrizos
Pharmacophore Mapping Of Thienopyrimidine-Based Monophosphonate (Thp-Mp) Inhibitors Of The Human Farnesyl Pyrophosphate Synthase.
J. Med. Chem. V. 60 2119 2017
PubMed-ID: 28208018  |  Reference-DOI: 10.1021/ACS.JMEDCHEM.6B01888

(-) Compounds

Molecule 1 - FARNESYL PYROPHOSPHATE SYNTHASE
    Chains: F
    EC Number: 2.5.1.10, 2.5.1.1
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: UNP RESIDUES 67-419
    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, 5)

Asymmetric Unit (3, 5)
No.NameCountTypeFull Name
16O32Ligand/Ion{[6-(4-METHYLPHENYL)THIENO[2,3-D]PYRIMIDIN-5-YL]METHYL}PHOSPHONIC ACID
2CL2Ligand/IonCHLORIDE ION
3PO41Ligand/IonPHOSPHATE ION
Biological Unit 1 (2, 6)
No.NameCountTypeFull Name
16O34Ligand/Ion{[6-(4-METHYLPHENYL)THIENO[2,3-D]PYRIMIDIN-5-YL]METHYL}PHOSPHONIC ACID
2CL-1Ligand/IonCHLORIDE ION
3PO42Ligand/IonPHOSPHATE ION

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY F:56 , LYS F:57 , GLN F:96 , ARG F:113 , 6O3 F:404 , HOH F:521 , HOH F:531binding site for residue PO4 F 401
2AC2SOFTWAREASP F:80binding site for residue CL F 402
3AC3SOFTWAREGLN F:115 , ILE F:116 , ARG F:346binding site for residue CL F 403
4AC4SOFTWARELYS F:57 , ASN F:59 , ARG F:60 , THR F:63 , SER F:205 , PHE F:206 , PHE F:239 , LYS F:347 , PO4 F:401 , HOH F:508binding site for residue 6O3 F 404
5AC5SOFTWARETHR F:111 , GLY F:114 , GLN F:115 , ILE F:116 , TYR F:322 , ARG F:346 , TYR F:349 , HOH F:502binding site for residue 6O3 F 405

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5JV2)

(-) 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 5JV2)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5JV2)

(-) Exons   (0, 0)

(no "Exon" information available for 5JV2)

(-) Sequences/Alignments

Asymmetric Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
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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:331
                                                                                                                                                                                                                                                                                                                                                                           
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...ee..ee.hhhh..hhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhh..........hhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.............hhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5jv2 F  10 YAQEKQDFVQHFSQIVRVLTEPEIGDAIARLKEVLEYNAIGGKYNRGLTVVVAFRELVPRKQDADSLQRAWTVGWCVELLQAFFLVADDIMDSSLTRRGQICWYQKPGVGLDAINDANLLEACIYRLLKLYCREQPYYLNLIELFLQSSYQTEIGQTLDLLTAPQGNVDLVRFTEKRYKSIVKYKTAFYSFYLPIAAAMYMAGIDGEKEHANAKKILLEMGEFFQIQDDYLDLFGDPKIGTDIQDNKCSWLVVQCLQRATPEQYQILKENYGQKEAEKVARVKALYEELDLPAVFLQYEEDSYSHIMALIEQYAAPLPPAVFLGLARKIYK 350
                                    19        29||      44        54        64       |75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245      |259       269       279       289       299       309       319       329       339       349 
                                               30|                                  72|                                                                                                                                                                               252|                                                                                             
                                                36                                   74                                                                                                                                                                                257
   Legend:   → Mismatch (orange background)
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  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 5JV2)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5JV2)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5JV2)

(-) Gene Ontology  (17, 17)

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  Cis Peptide Bonds
    Ala F:334 - Pro F:335   [ RasMol ]  
 
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  5jv2
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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 5djr 5djv 5ja0 5juz 5jv0 5jv1 5ksx

(-) Related Entries Specified in the PDB File

5juz 5jv0 5jv1