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(-) Description

Title :  CRYSTAL STRUCTURE OF PLASMODIUM VIVAX GERANYLGERANYLPYROPHOSPHATE SYNTHASE COMPLEXED WITH BPH-1182
 
Authors :  Y. -L. Liu, Y. Zhang, E. Oldfield
Date :  18 Jan 16  (Deposition) - 07 Sep 16  (Release) - 21 Sep 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.70
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,C  (1x)
Biol. Unit 2:  B,D  (1x)
Keywords :  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 Taxid: 562
    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): A C 
Biological Unit 2 (1x):  B D

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 5)

Asymmetric Unit (2, 5)
No.NameCountTypeFull Name
1HXK4Ligand/Ion2-{[3-HYDROXY-5-(OCTYLOXY)BENZYL]SULFANYL}BENZOIC ACID
2SO41Ligand/IonSULFATE ION
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name
1HXK2Ligand/Ion2-{[3-HYDROXY-5-(OCTYLOXY)BENZYL]SULFANYL}BENZOIC ACID
2SO4-1Ligand/IonSULFATE ION
Biological Unit 2 (2, 3)
No.NameCountTypeFull Name
1HXK2Ligand/Ion2-{[3-HYDROXY-5-(OCTYLOXY)BENZYL]SULFANYL}BENZOIC ACID
2SO41Ligand/IonSULFATE ION

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY A:80 , LYS A:81 , ASN A:82 , ARG A:84 , GLN A:119 , LEU A:123 , ARG A:136 , LYS A:243 , THR A:244 , TYR A:247 , HOH A:503 , HOH A:512 , ASN C:154 , LEU C:157binding site for residue HXK A 401
2AC2SOFTWAREGLY B:80 , LYS B:81 , ARG B:84 , GLN B:119 , PHE B:122 , LEU B:123 , ALA B:125 , ARG B:136 , LYS B:243 , THR B:244 , TYR B:247 , SER B:248 , LEU D:157binding site for residue HXK B 401
3AC3SOFTWAREASN A:154 , LEU A:157 , GLY C:80 , LYS C:81 , ARG C:84 , GLN C:119 , PHE C:122 , ARG C:135 , ARG C:136 , LYS C:243 , TYR C:247 , GLN C:284 , ASP C:287 , HOH C:506binding site for residue HXK C 401
4AC4SOFTWAREASN B:154 , LEU B:157 , ARG D:84 , GLN D:119 , PHE D:122 , THR D:244 , TYR D:247 , GLY D:280 , PHE D:283 , GLN D:284 , ASP D:287 , SO4 D:402 , HOH D:501binding site for residue HXK D 401
5AC5SOFTWAREGLY D:80 , LYS D:81 , GLN D:119 , ARG D:136 , HXK D:401 , HOH D:501 , HOH D:531binding site for residue SO4 D 402

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5HN8)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 5HN8)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5HN8)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5HN8)

(-) Exons   (0, 0)

(no "Exon" information available for 5HN8)

(-) 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:321
                                                                                                                                                                                                                                                                                                                                                                 
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...ee..ee.hhhh..hhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhh.....................hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhh........hhhhhhhhh....hhhhhh....hhhhhhhh.hhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5hn8 A  34 LAFFRNMYDKYRDAFLSHLNEYSLEEEIKEHISKYYKLLFDYNCLGGKNNRGILVILIYEYINSSEWEKAACLAWCIEILQAAFLVADDIMDKGEMRRNKYCWYLLKDVETKNAVNDVLLLYNSIYKLIEIYLRNESCYVDVIATFRDATLKTIIGQHLDTNIFSDKYSDIDVNNINVPEQPVIDINMINFGVYKNIVIHKTAYYSFFLPIVCGMLLAGIDNLIYKKIEDISMLMGEYFQIHDDYLDSDIQNNKLTWPLIKTFELCPDKIIVKNYGKVIDSLYEQYKHYESYEKAQKAKILSAIELHHEGIEYVLKYLLEI 391
                                    43        53        63        73        83        93||     108       118       128       138       148       158       168       178       188       198       208|      222       232       242       252       262|      274       284      |306       316     ||328|     |346     ||359       369   ||  380       390 
                                                                                       94|                                                                                                         208|                                              262|                       291|               322|  ||   336|     352|              373|                
                                                                                       100                                                                                                          213                                               265                        304                325  ||    344      356               375                
                                                                                                                                                                                                                                                                                                       328|                                                  
                                                                                                                                                                                                                                                                                                        330                                                  


Chain B from PDB  Type:PROTEIN  Length:326
                                                                                                                                                                                                                                                                                                                                                                      
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..ee..ee.hhhh..hhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhh.................hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhh..hhhhhhhhhhhh.....hhhhhhh..hhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5hn8 B  35 AFFRNMYDKYRDAFLSHLNEYSLEEEIKEHISKYYKLLFDYNCLGGKNNRGILVILIYEYVKDINSSEWEKAACLAWCIEILQAAFLVADDIMDKGEMRRNKYCWYLLKDVETKNAVNDVLLLYNSIYKLIEIYLRNESCYVDVIATFRDATLKTIIGQHLDTNIFSDKYREIDVNNINPVIDINMINFGVYKNIVIHKTAYYSFFLPIVCGMLLAGIDNLIYKKIEDISMLMGEYFQIHDDYLDINNKLTWPLIKTFELCSEPDKIKIVKNYGNLAKVIDSLYEQYKIRKHYESYEKAQKAKILSAINELHHEGIEYVLKYLLEI 391
                                    44        54        64        74        84        94 ||    106       116       126       136       146       156       166       176       186       196       206|      224       234       244       254       266       276       286     ||311       321       331   || |345       355       365       375       385      
                                                                                        96|                                                                                                        206|     219|                                   262|                        292|                        335| ||                                                
                                                                                         99                                                                                                         211      224                                    265                         308                         338 ||                                                
                                                                                                                                                                                                                                                                                                              340|                                                
                                                                                                                                                                                                                                                                                                               343                                                


Chain C from PDB  Type:PROTEIN  Length:334
                                                                                                                                                                                                                                                                                                                                                                              
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh........hhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhh.......................hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhh..........hhhhhhhhh..hhhhhhhhhhhh...hhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5hn8 C  37 FRNMYDKYRDAFLSHLNEEEEIKEHISKYYKLLFDYNCLGGKNNRGILVILIYEYVINSSEWEKAACLAWCIEILQAAFLVADDIMDKGEMRRNKYCWYLLKDVETKNAVNDVLLLYNSIYKLIEIYLRNESCYVDVIATFRDATLKTIIGQHLDTNIFSDKYDAREIDVNNINVPEQPVIDINMINFGVYKNIVIHKTAYYSFFLPIVCGMLLAGIDNLIYKKIEDISMLMGEYFQIHDDYLDIFSDIQNNKLTWPLIKTFELCSEPDKIKIVKNYGKNNLACVKVIDSLYQYKIRKHYESYEKAQKAKILSAINELHHEGIEYVLKYLLEIL 392
                                    46       |59        69        79        89     ||103       113       123       133       143       153       163       173       183       193       203  |||| 215       225       235       245       255      |267       277       287     ||307       317       327       337       347 ||    358       368       378       388    
                                            54|                                   95|                                                                                                       206|||                                                262|                         293|                                          349|                                         
                                             58                                   100                                                                                                        208||                                                 265                          304                                           351                                         
                                                                                                                                                                                              209|                                                                                                                                                                        
                                                                                                                                                                                               211                                                                                                                                                                        


Chain D from PDB  Type:PROTEIN  Length:334
                                                                                                                                                                                                                                                                                                                                                                              
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhh...hhhhhhhhh.hhhhhhhhhh...hhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..ee..ee.hhhh..hhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhh...................hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhh........hhhhhhhhh..hhhhhhhhhhhh...hhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5hn8 D  34 LAFFRNMYDKYRDAFLSHLNEYSLEEEIKEHISYYKLLFDYNCLGGKNNRGILVILIYEYVINSSEWEKAACLAWCIEILQAAFLVADDIMDKGEMRRNKYCWYLLKDVETKNAVNDVLLLYNSIYKLIEIYLRNESCYVDVIATFRDATLKTIIGQHLDTNIFSDKYSEIDVNNINVPPVIDINMINFGVYKNIVIHKTAYYSFFLPIVCGMLLAGIDNLIYKKIEDISMLMGEYFQIHDDYLSDIQNNKLTWPLIKTFELCSEPDKIKIVKNYGKNNLACVKVIDSLYEQYKIRKHYESYEKAQKAKILSAINELHHEGIEYVLKYLLEILF 393
                                    43        53        63  ||    74        84        94||     108       118       128       138       148       158       168       178       188       198       212       224       234       244       254       266       276       286   ||  309       319       329       339       349       359       369       379       389    
                                                           66|                         95|                                                                                                        207|      221|                                   262|                      290|                                                                                         
                                                            68                         100                                                                                                         212       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 5HN8)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5HN8)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5HN8)

(-) 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 5hn9 5hna

(-) Related Entries Specified in the PDB File

5hn7 5hn9 5hna