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(-) Description

Title :  CRYSTAL STRUCTURE OF PLASMODIUM VIVAX GERANYLGERANYLPYROPHOSPHATE SYNTHASE COMPLEXED WITH BPH-1251
 
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 :  2.69
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
Keywords :  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
163D4Ligand/Ion4-CHLORO-2-{[3-(DECYLOXY)-5-HYDROXYBENZYL]OXY}-5-SULFAMOYLBENZOIC ACID
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name
163D2Ligand/Ion4-CHLORO-2-{[3-(DECYLOXY)-5-HYDROXYBENZYL]OXY}-5-SULFAMOYLBENZOIC ACID
Biological Unit 2 (1, 2)
No.NameCountTypeFull Name
163D2Ligand/Ion4-CHLORO-2-{[3-(DECYLOXY)-5-HYDROXYBENZYL]OXY}-5-SULFAMOYLBENZOIC ACID

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELYS A:81 , ARG A:84 , GLN A:119 , PHE A:122 , LEU A:123 , ALA A:125 , MET A:129 , ARG A:135 , ARG A:136 , TYR A:160 , GLN A:195 , LYS A:243 , TYR A:247 , PHE A:283 , GLN A:284 , HOH A:536 , ASN B:154 , LEU B:157binding site for residue 63D A 401
2AC2SOFTWAREASN A:154 , LEU A:157 , GLY B:80 , LYS B:81 , ARG B:84 , GLN B:119 , ALA B:121 , PHE B:122 , LEU B:123 , MET B:129 , ARG B:135 , ARG B:136 , TYR B:160 , GLN B:195 , LYS B:243 , PHE B:283 , GLN B:284binding site for residue 63D B 401
3AC3SOFTWARELYS C:81 , ARG C:84 , GLN C:119 , ALA C:121 , PHE C:122 , LEU C:123 , ARG C:135 , ARG C:136 , TYR C:160 , GLN C:195 , LYS C:243 , PHE C:283 , GLN C:284 , ASN D:154 , LEU D:157binding site for residue 63D C 401
4AC4SOFTWAREASN C:154 , LEU C:157 , GLY D:80 , LYS D:81 , ARG D:84 , GLN D:119 , ALA D:121 , PHE D:122 , LEU D:123 , MET D:129 , ARG D:135 , ARG D:136 , TYR D:160 , GLN D:195 , LYS D:243 , PHE D:283 , GLN D:284 , HOH D:506binding site for residue 63D D 401

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5HNA)

(-) 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:352
                                                                                                                                                                                                                                                                                                                                                                                                
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...ee..ee.hhhh..hhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhh................hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhh..........hhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5hna A  34 LAFFRNMYDKYRDAFLSHLNEYSLEEEIKEHISKYYKLLFDYNCLGGKNNRGILVILIYEYVKDINSSEWEKAACLAWCIEILQAAFLVADDIMDKGEMRRNKYCWYLLKDVETKNAVNDVLLLYNSIYKLIEIYLRNESCYVDVIATFRDATLKTIIGQHLDTNIFSDKYSREIDVNNINVPEQPVIDINMINFGVYKNIVIHKTAYYSFFLPIVCGMLLAGIDNLIYKKIEDISMLMGEYFQIHDDYLDIFDSTKTGKVSDIQNNKLTWPLIKTFELCSEPDKIKIVKNYGKNNLACVKVIDSLYEQYKIRKHYESYEKAQKAKILSAINELHHEGIEYVLKYLLEILFT 394
                                    43        53        63        73        83        93  ||   105       115       125       135       145       155       165       175       185       195       205 ||    218       228       238       248       258   ||  270       280       290  ||   301||     312       322       332       342       352       362       372       382       392  
                                                                                         96|                                                                                                         207|                                                262|                         293|    302|                                                                                          
                                                                                          99                                                                                                          211                                                 265                          295     304                                                                                          


Chain B from PDB  Type:PROTEIN  Length:352
                                                                                                                                                                                                                                                                                                                                                                                                
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...ee..ee.hhhh..hhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhh................hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhh..........hhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5hna B  34 LAFFRNMYDKYRDAFLSHLNEYSLEEEIKEHISKYYKLLFDYNCLGGKNNRGILVILIYEYVKDINSSEWEKAACLAWCIEILQAAFLVADDIMDKGEMRRNKYCWYLLKDVETKNAVNDVLLLYNSIYKLIEIYLRNESCYVDVIATFRDATLKTIIGQHLDTNIFSDKYSREIDVNNINVPEQPVIDINMINFGVYKNIVIHKTAYYSFFLPIVCGMLLAGIDNLIYKKIEDISMLMGEYFQIHDDYLDIFDSTKTGKVSDIQNNKLTWPLIKTFELCSEPDKIKIVKNYGKNNLACVKVIDSLYEQYKIRKHYESYEKAQKAKILSAINELHHEGIEYVLKYLLEILFT 394
                                    43        53        63        73        83        93  ||   105       115       125       135       145       155       165       175       185       195       205 ||    218       228       238       248       258   ||  270       280       290  ||   301||     312       322       332       342       352       362       372       382       392  
                                                                                         96|                                                                                                         207|                                                262|                         293|    302|                                                                                          
                                                                                          99                                                                                                          211                                                 265                          295     304                                                                                          


Chain C from PDB  Type:PROTEIN  Length:352
                                                                                                                                                                                                                                                                                                                                                                                                
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...ee..ee.hhhh..hhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhh................hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhh..........hhhhhhhhhh...hhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5hna C  34 LAFFRNMYDKYRDAFLSHLNEYSLEEEIKEHISKYYKLLFDYNCLGGKNNRGILVILIYEYVKDINSSEWEKAACLAWCIEILQAAFLVADDIMDKGEMRRNKYCWYLLKDVETKNAVNDVLLLYNSIYKLIEIYLRNESCYVDVIATFRDATLKTIIGQHLDTNIFSDKYSREIDVNNINVPEQPVIDINMINFGVYKNIVIHKTAYYSFFLPIVCGMLLAGIDNLIYKKIEDISMLMGEYFQIHDDYLDIFDSTKTGKVSDIQNNKLTWPLIKTFELCSEPDKIKIVKNYGKNNLACVKVIDSLYEQYKIRKHYESYEKAQKAKILSAINELHHEGIEYVLKYLLEILFT 394
                                    43        53        63        73        83        93  ||   105       115       125       135       145       155       165       175       185       195       205 ||    218       228       238       248       258   ||  270       280       290  ||   301||     312       322       332       342       352       362       372       382       392  
                                                                                         96|                                                                                                         207|                                                262|                         293|    302|                                                                                          
                                                                                          99                                                                                                          211                                                 265                          295     304                                                                                          


Chain D from PDB  Type:PROTEIN  Length:352
                                                                                                                                                                                                                                                                                                                                                                                                
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...ee..ee.hhhh..hhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhh................hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhh..........hhhhhhhhhh.hhhhhhhhhhhh...hhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5hna D  34 LAFFRNMYDKYRDAFLSHLNEYSLEEEIKEHISKYYKLLFDYNCLGGKNNRGILVILIYEYVKDINSSEWEKAACLAWCIEILQAAFLVADDIMDKGEMRRNKYCWYLLKDVETKNAVNDVLLLYNSIYKLIEIYLRNESCYVDVIATFRDATLKTIIGQHLDTNIFSDKYSREIDVNNINVPEQPVIDINMINFGVYKNIVIHKTAYYSFFLPIVCGMLLAGIDNLIYKKIEDISMLMGEYFQIHDDYLDIFDSTKTGKVSDIQNNKLTWPLIKTFELCSEPDKIKIVKNYGKNNLACVKVIDSLYEQYKIRKHYESYEKAQKAKILSAINELHHEGIEYVLKYLLEILFT 394
                                    43        53        63        73        83        93  ||   105       115       125       135       145       155       165       175       185       195       205 ||    218       228       238       248       258   ||  270       280       290  ||   301||     312       322       332       342       352       362       372       382       392  
                                                                                         96|                                                                                                         207|                                                262|                         293|    302|                                                                                          
                                                                                          99                                                                                                          211                                                 265                          295     304
   Legend:   → Mismatch (orange background)
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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  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (5, 5)

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        A5K4U6_PLAVS | A5K4U6: 3cc9 3ez3 3ldw 3mav 3ph7 3rbm 3ryw 5hn7 5hn8 5hn9

(-) Related Entries Specified in the PDB File

5hn7 5hn8 5hn9