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(-) Description

Title :  CRYSTAL STRUCTURE OF HUMAN FPPS IN TERNARY COMPLEX WITH YS0470 AND ISOPENTENYL PYROPHOSPHATE
 
Authors :  J. Park, Y. -S. Lin, Y. S. Tsantrizos, A. M. Berghuis
Date :  18 Sep 12  (Deposition) - 26 Dec 12  (Release) - 26 Dec 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.04
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, Y. S. Lin, J. W. De Schutter, Y. S. Tsantrizos, A. M. Berghuis
Ternary Complex Structures Of Human Farnesyl Pyrophosphate Synthase Bound With A Novel Inhibitor And Secondary Ligands Provide Insights Into The Molecular Details Of The Enzyme'S Active Site Closure.
Bmc Struct. Biol. V. 12 32 2012
PubMed-ID: 23234314  |  Reference-DOI: 10.1186/1472-6807-12-32

(-) Compounds

Molecule 1 - FARNESYL PYROPHOSPHATE SYNTHASE
    Chains: F
    EC Number: 2.5.1.1, 2.5.1.10
    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: FPP SYNTHASE, 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
1IPR1Ligand/IonISOPENTYL PYROPHOSPHATE
2MG3Ligand/IonMAGNESIUM ION
3YS41Ligand/Ion[({4-[4-(PROPAN-2-YLOXY)PHENYL]PYRIDIN-2-YL}AMINO)METHANEDIYL]BIS(PHOSPHONIC ACID)
Biological Unit 1 (2, 4)
No.NameCountTypeFull Name
1IPR2Ligand/IonISOPENTYL PYROPHOSPHATE
2MG-1Ligand/IonMAGNESIUM ION
3YS42Ligand/Ion[({4-[4-(PROPAN-2-YLOXY)PHENYL]PYRIDIN-2-YL}AMINO)METHANEDIYL]BIS(PHOSPHONIC ACID)

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREPHE F:98 , PHE F:99 , ALA F:102 , ASP F:103 , ASP F:107 , ARG F:112 , ASN F:130 , ASN F:133 , THR F:167 , GLN F:171 , LYS F:200 , THR F:201 , ASP F:243 , LYS F:257 , IPR F:402 , MG F:403 , MG F:404 , MG F:405 , HOH F:501 , HOH F:503 , HOH F:505 , HOH F:506 , HOH F:507 , HOH F:508 , HOH F:519 , HOH F:538 , HOH F:564BINDING SITE FOR RESIDUE YS4 F 401
2AC2SOFTWAREGLY F:56 , LYS F:57 , ARG F:60 , GLN F:96 , ARG F:113 , THR F:201 , TYR F:204 , PHE F:239 , GLN F:240 , ASP F:243 , YS4 F:401 , HOH F:509 , HOH F:510 , HOH F:522 , HOH F:525 , HOH F:535 , HOH F:543 , HOH F:566BINDING SITE FOR RESIDUE IPR F 402
3AC3SOFTWAREASP F:103 , ASP F:107 , YS4 F:401 , MG F:405 , HOH F:503 , HOH F:504 , HOH F:505BINDING SITE FOR RESIDUE MG F 403
4AC4SOFTWAREASP F:243 , YS4 F:401 , HOH F:506 , HOH F:507 , HOH F:508BINDING SITE FOR RESIDUE MG F 404
5AC5SOFTWAREASP F:103 , ASP F:107 , YS4 F:401 , MG F:403 , HOH F:501 , HOH F:564BINDING SITE FOR RESIDUE MG F 405

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4H5E)

(-) 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 4H5E)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4H5E)

(-) Exons   (0, 0)

(no "Exon" information available for 4H5E)

(-) Sequences/Alignments

Asymmetric Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
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   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:346
                                                                                                                                                                                                                                                                                                                                                                                          
               SCOP domains d4h5ef_ F: automated matches                                                                                                                                                                                                                                                                                                                               SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...ee..ee.hhhh..hhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...........hhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4h5e F   8 DVYAQEKQDFVQHFSQIVRVLTEDEMGHPEIGDAIARLKEVLEYNAIGGKYNRGLTVVVAFRELVEPRKQDADSLQRAWTVGWCVELLQAFFLVADDIMDSSLTRRGQICWYQKPGVGLDAINDANLLEACIYRLLKLYCREQPYYLNLIELFLQSSYQTEIGQTLDLLTAPQGNVDLVRFTEKRYKSIVKYKTAFYSFYLPIAAAMYMAGIDGEKEHANAKKILLEMGEFFQIQDDYLDLFGDPSVTGKIGTDIQDNKCSWLVVQCLQRATPEQYQILKENYGQKEAEKVARVKALYEELDLPAVFLQYEEDSYSHIMALIEQYAAPLPPAVFLGLARKIYKRRK 353
                                    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       307       317       327       337       347
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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  (1, 1)

Asymmetric Unit
(-)
Class: All alpha proteins (14657)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4H5E)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4H5E)

(-) Gene Ontology  (17, 17)

Asymmetric Unit(hide GO term definitions)

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    Ala F:334 - Pro F:335   [ RasMol ]  
 
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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 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 5jv2 5ksx

(-) Related Entries Specified in the PDB File

4dem CRYSTAL STRUCTURE OF THE SAME PROTEIN IN BINARY COMPLEX WITH YS0470
4h5c
4h5d