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(-) Description

Title :  T. BRUCEI FARNESYL DIPHOSPHATE SYNTHASE COMPLEXED WITH BISPHOSPHONATE BPH-527
 
Authors :  R. Cao, Y. Gao, H. Robinson, A. Goddard, E. Oldfield
Date :  05 Jan 07  (Deposition) - 02 Oct 07  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Protein-Bisphosphonate Complex, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Y. Zhang, R. Cao, A. Leon, R. T. Guo, K. Krysiak, F. Yin, M. P. Hudock, S. Mukherjee, Y. Gao, H. Robinson, Y. Song, J. H. No, W. Hong, C. Morita, A. H. -J. Wang, E. Oldfield
Bisphosphonates: Teaching Old Drugs With New Tricks
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - FARNESYL PYROPHOSPHATE SYNTHASE
    Chains: A, B
    EC Number: 2.5.1.10
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Organism Scientific: TRYPANOSOMA BRUCEI
    Organism Taxid: 5691

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 16)

Asymmetric/Biological Unit (5, 16)
No.NameCountTypeFull Name
1ACT4Ligand/IonACETATE ION
2BME3Ligand/IonBETA-MERCAPTOETHANOL
3MG6Ligand/IonMAGNESIUM ION
4MPD1Ligand/Ion(4S)-2-METHYL-2,4-PENTANEDIOL
5SUF2Ligand/Ion[2-(DIMETHYL-LAMBDA~4~-SULFANYL)-1-HYDROXYETHANE-1,1-DIYL]BIS(PHOSPHONIC ACID)

(-) Sites  (0, 0)

(no "Site" information available for 2OGD)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 2OGD)

(-) Sequences/Alignments

Asymmetric/Biological 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:358
 aligned with Q86C09_9TRYP | Q86C09 from UniProtKB/TrEMBL  Length:367

    Alignment length:367
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       
         Q86C09_9TRYP     1 MPMQMFMQVYDEIQMFLLEELELKFDMDPNRVRYLRKMMDTTCLGGKYNRGLTVIDVAESLLSLSPNNNGEEDDGARRKRVLHDACVCGWMIEFLQAHYLVEDDIMDNSVTRRGKPCWYRHPDVTVQCAINDGLLLKSWTHMMAMHFFADRPFLQDLLCRFNRVDYTTAVGQLYDVTSMFDSNKLDPDVSQPTTTDFAEFTLSNYKRIVKYKTAYYTYLLPLVMGLIVSEALPTVDMGVTEELAMLMGEYFQVQDDVMDCFTPPERLGKVGTDIQDAKCSWLAVTFLAKASSAQVAEFKANYGSGDSEKVATVRRLYEEADLQGDYVAYEAAVAEQVKELIEKLRLCSPGFAASVETLWGKTYKRQK 367
               SCOP domains d2ogda_ A: automated matches                                                                                                                                                                                                                                                                                                                                                    SCOP domains
               CATH domains 2ogdA00 A:1-367 Farnesyl Diphosphate Synthase                                                                                                                                                                                                                                                                                                                                   CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhh..---------.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...ee..ee.hhhh...hhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhh...hhhhh...............hhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...........hhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2ogd A   1 MPMQMFMQVYDEIQMFLLEELELKFDMDPNRVRYLRKMMDTTCLGGKYNRGLTVIDVAESLLSL---------DGARRKRVLHDACVCGWMIEFLQAHYLVEDDIMDNSVTRRGKPCWYRHPDVTVQCAINDGLLLKSWTHMMAMHFFADRPFLQDLLCRFNRVDYTTAVGQLYDVTSMFDSNKLDPDVSQPTTTDFAEFTLSNYKRIVKYKTAYYTYLLPLVMGLIVSEALPTVDMGVTEELAMLMGEYFQVQDDVMDCFTPPERLGKVGTDIQDAKCSWLAVTFLAKASSAQVAEFKANYGSGDSEKVATVRRLYEEADLQGDYVAYEAAVAEQVKELIEKLRLCSPGFAASVETLWGKTYKRQK 367
                                    10        20        30        40        50        60   |     -   |    80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       
                                                                                          64        74                                                                                                                                                                                                                                                                                                     


Chain B from PDB  Type:PROTEIN  Length:359
 aligned with Q86C09_9TRYP | Q86C09 from UniProtKB/TrEMBL  Length:367

    Alignment length:367
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       
         Q86C09_9TRYP     1 MPMQMFMQVYDEIQMFLLEELELKFDMDPNRVRYLRKMMDTTCLGGKYNRGLTVIDVAESLLSLSPNNNGEEDDGARRKRVLHDACVCGWMIEFLQAHYLVEDDIMDNSVTRRGKPCWYRHPDVTVQCAINDGLLLKSWTHMMAMHFFADRPFLQDLLCRFNRVDYTTAVGQLYDVTSMFDSNKLDPDVSQPTTTDFAEFTLSNYKRIVKYKTAYYTYLLPLVMGLIVSEALPTVDMGVTEELAMLMGEYFQVQDDVMDCFTPPERLGKVGTDIQDAKCSWLAVTFLAKASSAQVAEFKANYGSGDSEKVATVRRLYEEADLQGDYVAYEAAVAEQVKELIEKLRLCSPGFAASVETLWGKTYKRQK 367
               SCOP domains d2ogdb_ B: automated matches                                                                                                                                                                                                                                                                                                                                                    SCOP domains
               CATH domains 2ogdB00 B:1-367 Farnesyl Diphosphate Synthase                                                                                                                                                                                                                                                                                                                                   CATH domains
           Pfam domains (1) ---------------------------------polyprenyl_synt-2ogdB01 B:34-32        8                                                                                                                                                                                                                                                               --------------------------------------- Pfam domains (1)
           Pfam domains (2) ---------------------------------polyprenyl_synt-2ogdB02 B:34-32        8                                                                                                                                                                                                                                                               --------------------------------------- Pfam domains (2)
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhh..--------..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..ee..ee.hhhh...hhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhh...hhhhh...............hhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...........hhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2ogd B   1 MPMQMFMQVYDEIQMFLLEELELKFDMDPNRVRYLRKMMDTTCLGGKYNRGLTVIDVAESLLSL--------DDGARRKRVLHDACVCGWMIEFLQAHYLVEDDIMDNSVTRRGKPCWYRHPDVTVQCAINDGLLLKSWTHMMAMHFFADRPFLQDLLCRFNRVDYTTAVGQLYDVTSMFDSNKLDPDVSQPTTTDFAEFTLSNYKRIVKYKTAYYTYLLPLVMGLIVSEALPTVDMGVTEELAMLMGEYFQVQDDVMDCFTPPERLGKVGTDIQDAKCSWLAVTFLAKASSAQVAEFKANYGSGDSEKVATVRRLYEEADLQGDYVAYEAAVAEQVKELIEKLRLCSPGFAASVETLWGKTYKRQK 367
                                    10        20        30        40        50        60   |     -  |     80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       
                                                                                          64       73
   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  (1, 2)

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

(-) CATH Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Class: Mainly Alpha (13335)

(-) Pfam Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Clan: no clan defined [family: polyprenyl_synt] (86)

(-) Gene Ontology  (3, 3)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (Q86C09_9TRYP | Q86C09)
molecular function
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0016740    transferase activity    Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
biological process
    GO:0008299    isoprenoid biosynthetic process    The chemical reactions and pathways resulting in the formation of any isoprenoid compound, isoprene (2-methylbuta-1,3-diene) or compounds containing or derived from linked isoprene (3-methyl-2-butenylene) residues.

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 Related Entries

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

UniProtKB/TrEMBL
        Q86C09_9TRYP | Q86C09: 2ewg 2i19 2p1c 3dyf 3dyg 3dyh 3efq 3egt 4rxc 4rxd 4rxe 4ryp 5ael 5afx 5ahu

(-) Related Entries Specified in the PDB File

2ogc 2ogl