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(-) Description

Title :  CRYSTAL STRUCTURE OF PLASMODIUM VIVAX GERANYLGERANYLPYROPHOSPHATE SYNTHASE COMPLEXED WITH BPH-1186
 
Authors :  Y. -L. Liu, Y. Zhang, E. Oidfield
Date :  18 Jan 16  (Deposition) - 07 Sep 16  (Release) - 21 Sep 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.12
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
Keywords :  All Helices, Transferase, Transferase-Transferase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  C. G Ricci, Y. L. Liu, Y. Zhang, Y. Wang, W. Zhu, E. Oldfield, J. A. Mccammon
Dynamic Structure And Inhibition Of A Malaria Drug Target: Geranylgeranyl Diphosphate Synthase.
Biochemistry V. 55 5180 2016
PubMed-ID: 27564465  |  Reference-DOI: 10.1021/ACS.BIOCHEM.6B00398

(-) Compounds

Molecule 1 - FARNESYL PYROPHOSPHATE SYNTHASE, PUTATIVE
    Chains: A, B, C, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: P15-TEV-LIC
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: PVX_092040
    Organism Scientific: PLASMODIUM VIVAX
    Organism Taxid: 126793
    Strain: SALVADOR I

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): AB  
Biological Unit 2 (1x):   CD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 4)

Asymmetric Unit (1, 4)
No.NameCountTypeFull Name
104W4Ligand/Ion2-{[3-(DECYLOXY)BENZYL]OXY}-5-NITROBENZOIC ACID
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name
104W2Ligand/Ion2-{[3-(DECYLOXY)BENZYL]OXY}-5-NITROBENZOIC ACID
Biological Unit 2 (1, 2)
No.NameCountTypeFull Name
104W2Ligand/Ion2-{[3-(DECYLOXY)BENZYL]OXY}-5-NITROBENZOIC ACID

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY A:80 , LYS A:81 , ARG A:84 , GLN A:119 , PHE A:122 , LEU A:123 , MET A:129 , ARG A:135 , ARG A:136 , ILE A:192 , GLN A:195 , TYR A:247 , PHE A:283 , LYS A:301 , HOH A:502 , HOH A:547 , HOH A:566 , ASN B:154binding site for residue 04W A 401
2AC2SOFTWAREASN A:154 , LEU A:157 , GLY B:80 , LYS B:81 , ARG B:84 , GLN B:119 , PHE B:122 , LEU B:123 , MET B:129 , ARG B:135 , ARG B:136 , ILE B:192 , GLN B:195 , TYR B:247 , PHE B:283 , ASP B:287 , LYS B:301 , HOH B:513 , HOH B:561 , HOH B:597binding site for residue 04W B 401
3AC3SOFTWAREGLY C:80 , LYS C:81 , ARG C:84 , GLN C:119 , PHE C:122 , LEU C:123 , ALA C:125 , MET C:129 , ARG C:135 , ARG C:136 , ILE C:192 , GLN C:195 , TYR C:247 , PHE C:283 , LYS C:301 , HOH C:506 , HOH C:529 , ASN D:154 , LEU D:157binding site for residue 04W C 401
4AC4SOFTWAREASN C:154 , LEU C:157 , GLY D:80 , LYS D:81 , ARG D:84 , GLN D:119 , PHE D:122 , LEU D:123 , MET D:129 , ARG D:135 , ARG D:136 , ILE D:192 , LYS D:243 , TYR D:247 , PHE D:283 , LYS D:301 , HOH D:514 , HOH D:527 , HOH D:552binding site for residue 04W D 401

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5HN9)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 5HN9)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5HN9)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5HN9)

(-) Exons   (0, 0)

(no "Exon" information available for 5HN9)

(-) 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 A from PDB  Type:PROTEIN  Length:351
                                                                                                                                                                                                                                                                                                                                                                                               
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...ee..ee.hhhh..hhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhh...............hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhh..........hhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5hn9 A  36 FFRNMYDKYRDAFLSHLNEYSLEEEIKEHISKYYKLLFDYNCLGGKNNRGILVILIYEYVKRDINSSEWEKAACLAWCIEILQAAFLVADDIMDKGEMRRNKYCWYLLKDVETKNAVNDVLLLYNSIYKLIEIYLRNESCYVDVIATFRDATLKTIIGQHLDTNIFSDKYSEIDVNNINVPEQPVIDINMINFGVYKNIVIHKTAYYSFFLPIVCGMLLAGIDNLIYKKIEDISMLMGEYFQIHDDYLDIFDSTKTGKVSDIQNNKLTWPLIKTFELCSEPDKIKIVKNYGKNNLACVKVIDSLYEQYKIRKHYESYEKAQKAKILSAINELHHEGIEYVLKYLLEILFTG 395
                                    45        55        65        75        85        95||     106       116       126       136       146       156       166       176       186       196       206||     220       230       240       250       260 ||    272       282       292||     304       314       324       334       344       354       364       374       384       394 
                                                                                       96|                                                                                                          207|                                               262|                         293|    302|                                                                                           
                                                                                        98                                                                                                           212                                                265                          295     304                                                                                           


Chain B from PDB  Type:PROTEIN  Length:356
                                                                                                                                                                                                                                                                                                                                                                                                    
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...ee..ee.hhhh..hhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhh.................hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..........hhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5hn9 B  34 LAFFRNMYDKYRDAFLSHLNEYSLEEEIKEHISKYYKLLFDYNCLGGKNNRGILVILIYEYVKNRDINSSEWEKAACLAWCIEILQAAFLVADDIMDKGEMRRNKYCWYLLKDVETKNAVNDVLLLYNSIYKLIEIYLRNESCYVDVIATFRDATLKTIIGQHLDTNIFSDKYSDAREIDVNNINVPEQPVIDINMINFGVYKNIVIHKTAYYSFFLPIVCGMLLAGNLIYKKIEDISMLMGEYFQIHDDYLDIFGDSTKTGKVSDIQNNKLTWPLIKTFELCSEPDKIKIVKNYGKNNLACVKVIDSLYEQYKIRKHYESYEKAQKAKILSAINELHHEGIEYVLKYLLEILFTG 395
                                    43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203     ||214       224       234       244       254      |268       278       288       298   ||  309       319       329       339       349       359       369       379       389      
                                                                                                                                                                                                         209|                                               261|                                 302|                                                                                           
                                                                                                                                                                                                          211                                                266                                  304                                                                                           


Chain C from PDB  Type:PROTEIN  Length:334
                                                                                                                                                                                                                                                                                                                                                                              
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...ee..ee.hhhh..hhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhh..........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhh............hhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5hn9 C  37 FRNMYDKYRDAFLSHLNEYSLEEEIKEHISKYYKLLFDYNCLGGKNNRGILVILIYEYVINSSEWEKAACLAWCIEILQAAFLVADDIMDKGEMRRNKYCWYLLKDVETKNAVNDVLLLYNSIYKLIEIYLRNESCYVDVIATFRDATLKTIIGQHLDTNIFSDKYSIDVNNIQPVIDINMINFGVYKNIVIHKTAYYSFFLPIVCGMLLAGIDNLIYKKIEDISMLMGEYFQIHDDYLDITGKVSDIQNNKLTWPLIKTFELCSEPDKIKIVKNYGKNNLACVKVIDSLYEQYKIRKHYESYEKAQKAKILSAINELHHEGIEYVLKYLLEIL 392
                                    46        56        66        76        86       100       110       120       130       140       150       160       170       180       190       200      |215  ||   229       239       249       259  ||   271       281       291||  || 308       318       328       338       348       358       368       378       388    
                                                                                     95|                                                                                                        207|  218|                                    262|                        292|  ||                                                                                        
                                                                                     100                                                                                                         213   223                                     265                         299  ||                                                                                        
                                                                                                                                                                                                                                                                              302|                                                                                        
                                                                                                                                                                                                                                                                               304                                                                                        


Chain D from PDB  Type:PROTEIN  Length:347
                                                                                                                                                                                                                                                                                                                                                                                           
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...ee..ee.hhhh..hhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhh...............hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..........hhhhhhhhh..hhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5hn9 D  35 AFFRNMYDKYRDAFLSHLNEYSLEEEIKEHISKYYKLLFDYNCLGGKNNRGILVILIYEYVKNRINSSEWEKAACLAWCIEILQAAFLVADDIMDKGEMRRNKYCWYLLKDVETKNAVNDVLLLYNSIYKLIEIYLRNESCYVDVIATFRDATLKTIIGQHLDTNIFSDKYIDVNNINPVIDINMINFGVYKNIVIHKTAYYSFFLPIVCGMLLAGIDNLIYKKIEDISMLMGEYFQIHDDYLDIFGDSTKTGKVSDIQNNKLTWPLIKTFELCSEPDKIKIVKNYGKNNLACVKVIDSLYEQYKIRKHYESYEKAQKAKILSAINELHHEGIEYVLKYLLEILFTG 395
                                    44        54        64        74        84        94   ||  105       115       125       135       145       155       165       175       185       195       205||     225       235       245       255      |267       277       287       297    || 308       318       328       338       348       358       368       378       388       
                                                                                          98|                                                                                                       206|   219|                                   262|                                  302|                                                                                           
                                                                                          100                                                                                                        213    224                                    265                                   304
   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  (0, 0)

(no "SCOP Domain" information available for 5HN9)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5HN9)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5HN9)

(-) Gene Ontology  (5, 5)

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 Related Entries

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

UniProtKB/TrEMBL
        A5K4U6_PLAVS | A5K4U6: 3cc9 3ez3 3ldw 3mav 3ph7 3rbm 3ryw 5hn7 5hn8 5hna

(-) Related Entries Specified in the PDB File

5hn7 5hn8 5hna