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(-) Description

Title :  T. BRUCEI FARNESYL DIPHOSPHATE SYNTHASE COMPLEXED WITH BISPHOSPHONATE
 
Authors :  R. Cao, J. Mao, Y. Gao, H. Robinson, S. Odeh, A. Goddard, E. Oldfield
Date :  13 Aug 06  (Deposition) - 17 Oct 06  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.28
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Protein-Bisphosphonate Complex, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. Mao, S. Mukherjee, Y. Zhang, R. Cao, J. M. Sanders, Y. Song, Y. Zhang, G. A. Meints, Y. G. Gao, D. Mukkamala, M. P. Hudock, E. Oldfield
Solid-State Nmr, Crystallographic, And Computational Investigation Of Bisphosphonates And Farnesyl Diphosphate Synthase-Bisphosphonate Complexes.
J. Am. Chem. Soc. V. 128 14485 2006
PubMed-ID: 17090032  |  Reference-DOI: 10.1021/JA061737C
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - FARNESYL PYROPHOSPHATE SYNTHASE
    Chains: A, B
    EC Number: 2.5.1.10
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET-28A+
    Expression System Strain: BL21(DE3)-PLYSS
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    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  (2, 8)

Asymmetric/Biological Unit (2, 8)
No.NameCountTypeFull Name
11BY2Ligand/Ion[2-(PYRIDIN-2-YLAMINO)ETHANE-1,1-DIYL]BIS(PHOSPHONICACID)
2MG6Ligand/IonMAGNESIUM ION

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:103 , ASP A:107 , 1BY A:3001 , MG A:3003 , HOH A:5286BINDING SITE FOR RESIDUE MG A 3002
2AC2SOFTWAREASP A:103 , ASP A:107 , 1BY A:3001 , MG A:3002 , HOH A:5036BINDING SITE FOR RESIDUE MG A 3003
3AC3SOFTWAREASP A:255 , ASP A:259 , 1BY A:3001 , HOH A:5204BINDING SITE FOR RESIDUE MG A 3004
4AC4SOFTWAREASP B:103 , ASP B:107 , 1BY B:4001 , MG B:4004 , HOH B:5284BINDING SITE FOR RESIDUE MG B 4002
5AC5SOFTWAREASP B:255 , 1BY B:4001 , HOH B:5060 , HOH B:5203BINDING SITE FOR RESIDUE MG B 4003
6AC6SOFTWAREASP B:103 , ASP B:107 , ASP B:175 , 1BY B:4001 , MG B:4002 , HOH B:5031BINDING SITE FOR RESIDUE MG B 4004
7AC7SOFTWARETYR A:99 , LEU A:100 , ASP A:103 , ASP A:107 , ARG A:112 , THR A:168 , GLN A:172 , LYS A:212 , LYS A:269 , MG A:3002 , MG A:3003 , MG A:3004 , HOH A:5036 , HOH A:5204 , HOH A:5286BINDING SITE FOR RESIDUE 1BY A 3001
8AC8SOFTWARETYR B:99 , ASP B:103 , ASP B:107 , ARG B:112 , THR B:168 , GLN B:172 , LYS B:212 , MG B:4002 , MG B:4003 , MG B:4004 , HOH B:5031 , HOH B:5065 , HOH B:5113 , HOH B:5166 , HOH B:5203 , HOH B:5277 , HOH B:5284BINDING SITE FOR RESIDUE 1BY B 4001

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2I19)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2I19)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2I19)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2I19)

(-) Exons   (0, 0)

(no "Exon" information available for 2I19)

(-) 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:367
 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 d2i19a_ A: automated matches                                                                                                                                                                                                                                                                                                                                                    SCOP domains
               CATH domains 2i19A00 A:1-367 Farnesyl Diphosphate Synthase                                                                                                                                                                                                                                                                                                                                   CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhh...........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh........hhhhh...hhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhh...hhhhh...............hhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.................hhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2i19 A   1 MPMQMFMQVYDEIQMFLLEELELKFDMDPNRVRYLRKMMDTTCLGGKYNRGLTVIDVAESLLSLSPNNNGEEDDGARRKRVLHDACVCGWMIEFLQAHYLVEDDIMDNSVTRRGKPCWYRHPDVTVQCAINDGLLLKSWTHMMAMHFFADRPFLQDLLCRFNRVDYTTAVGQLYDVTSMFDSNKLDPDVSQPTTTDFAEFTLSNYKRIVKYKTAYYTYLLPLVMGLIVSEALPTVDMGVTEELAMLMGEYFQVQDDVMDCFTPPERLGKVGTDIQDAKCSWLAVTFLAKASSAQVAEFKANYGSGDSEKVATVRRLYEEADLQGDYVAYEAAVAEQVKELIEKLRLCSPGFAASVETLWGKTYKRQK 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       


Chain B from PDB  Type:PROTEIN  Length:361
 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 d2i19b_ B: automated matches                                                                                                                                                                                                                                                                                                                                                    SCOP domains
               CATH domains 2i19B00 B:1-367 Farnesyl Diphosphate Synthase                                                                                                                                                                                                                                                                                                                                   CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhh...------...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..ee..ee.hhhh...hhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhh...hhhhh...............hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...........hhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2i19 B   1 MPMQMFMQVYDEIQMFLLEELELKFDMDPNRVRYLRKMMDTTCLGGKYNRGLTVIDVAESLLSLS------EDDGARRKRVLHDACVCGWMIEFLQAHYLVEDDIMDNSVTRRGKPCWYRHPDVTVQCAINDGLLLKSWTHMMAMHFFADRPFLQDLLCRFNRVDYTTAVGQLYDVTSMFDSNKLDPDVSQPTTTDFAEFTLSNYKRIVKYKTAYYTYLLPLVMGLIVSEALPTVDMGVTEELAMLMGEYFQVQDDVMDCFTPPERLGKVGTDIQDAKCSWLAVTFLAKASSAQVAEFKANYGSGDSEKVATVRRLYEEADLQGDYVAYEAAVAEQVKELIEKLRLCSPGFAASVETLWGKTYKRQK 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       
                                                                                           65     72
   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  (0, 0)

(no "Pfam Domain" information available for 2I19)

(-) 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 2ogd 2p1c 3dyf 3dyg 3dyh 3efq 3egt 4rxc 4rxd 4rxe 4ryp 5ael 5afx 5ahu

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 2I19)