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(-) Description

Title :  TERNARY CO-CRYSTAL STRUCTURE OF FRUCTOSE-BISPHOSPHATE ALDOLASE FROM PLASMODIUM FALCIPARUM IN COMPLEX WITH TRAP AND A SMALL MOLECULE INHIBITOR
 
Authors :  G. Bosch, R. Weltzer, K. O'Malley, J. Bosch
Date :  15 Jun 14  (Deposition) - 26 Aug 15  (Release) - 02 Sep 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.11
Chains :  Asym./Biol. Unit :  A,B,C,D,E,G,H,I,J,K
Keywords :  Lyase-Lyase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. M. Nemetski, T. J. Cardozo, G. Bosch, R. Weltzer, K. O'Malley, I. Ejigiri, K. A. Kumar, C. A. Buscaglia, V. Nussenzweig, P. Sinnis, J. Levitskaya, J. Bosch
Inhibition By Stabilization: Targeting The Plasmodium Falciparum Aldolase-Trap Complex.
Malar. J. V. 14 324 2015
PubMed-ID: 26289816  |  Reference-DOI: 10.1186/S12936-015-0834-9
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - FRUCTOSE-BISPHOSPHATE ALDOLASE
    Chains: A, B, C, D
    EC Number: 4.1.2.13
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: PF14_0425
    Organism Scientific: PLASMODIUM FALCIPARUM
    Organism Taxid: 36329
    Strain: ISOLATE 3D7
 
Molecule 2 - ALA-ALA-SER-LEU-TYR-GLU-LYS-LYS-ALA-ALA
    Chains: E
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Organism Scientific: PLASMODIUM FALCIPARUM 3D7
    Organism Taxid: 36329
    Other Details: IT SEEMS AS IF THIS IS THE C-TERMINAL TAIL OF ALDOLASE, HOWEVER NO DIRECT CONNECTIVITY TO EITHER CHAIN A,B,C,D COULD BE MADE. AMINO ACIDS WERE MODELED AS GOOD AS POSSIBLE
 
Molecule 3 - ALA-ALA-ALA-SER-LEU-TYR-GLU-LYS-LYS-ALA-ALA
    Chains: G
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Organism Scientific: PLASMODIUM FALCIPARUM 3D7
    Organism Taxid: 36329
    Other Details: IT SEEMS AS IF THIS IS THE C-TERMINAL TAIL OF ALDOLASE, HOWEVER NO DIRECT CONNECTIVITY TO EITHER CHAIN A,B,C,D COULD BE MADE. AMINO ACIDS WERE MODELED AS GOOD AS POSSIBLE
 
Molecule 4 - ASP-TRP-ASN
    Chains: H, I, J, K
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Organism Scientific: PLASMODIUM FALCIPARUM 3D7
    Organism Taxid: 36329
    Other Details: SYNTHETIC TRAP-TAIL

 Structural Features

(-) Chains, Units

  12345678910
Asymmetric/Biological Unit : ABCDEGHIJK

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (1, 4)
No.NameCountTypeFull Name
138D4Ligand/IonN'-[(E)-(2,4-DICHLOROPHENYL)METHYLIDENE]-3,4-DIHYDROXYBENZOHYDRAZIDE

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:39 , THR A:44 , LYS A:151 , ARG A:153 , GLU A:194 , LYS A:236 , HOH A:525 , HOH A:527 , HOH A:564 , HOH A:618 , ASP H:604 , ASN H:606binding site for residue 38D A 401
2AC2SOFTWAREASP B:39 , SER B:41 , THR B:44 , LYS B:47 , LYS B:112 , LYS B:151 , ARG B:153 , HOH B:502 , HOH B:569 , HOH B:594 , ASP I:604 , ASN I:606 , HOH I:702binding site for residue 38D B 401
3AC3SOFTWAREASP C:39 , THR C:44 , LYS C:47 , LYS C:112 , LYS C:151 , HOH C:510 , HOH C:533 , HOH C:555 , HOH C:560 , HOH C:574 , HOH C:599 , HOH C:614 , ASN J:606binding site for residue 38D C 401
4AC4SOFTWAREASP D:39 , THR D:44 , ARG D:48 , LYS D:112 , LYS D:151 , ARG D:153 , ASP K:604 , TRP K:605 , ASN K:606 , HOH K:801binding site for residue 38D K 701

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4TR9)

(-) Cis Peptide Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1Lys A:164 -Pro A:165
2Lys B:164 -Pro B:165
3Lys C:164 -Pro C:165
4Lys D:164 -Pro D:165

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4TR9)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4TR9)

(-) Exons   (0, 0)

(no "Exon" information available for 4TR9)

(-) 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:347
                                                                                                                                                                                                                                                                                                                                                                                           
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........hhhhhhhhhhhhhhhh....eeeee..hhhhhhhhhhhh....hhhhhhhhhhhhhh..hhhh.eeeeeehhhhhh.......hhhhhhhhh..eeeee....eee.......eee....hhhhhhhhhhhhh..eeeeeeee..hhhhh..hhhhhhhhhhhhhhhhhhhhhh..eeeeeeee......hhhhhhhhhhhhhhhhhhhhhhh..hhhhhee...............hhhhhhhhhhhhhhhhh.....eeee.....hhhhhhhhhhhhhh......eeeeeehhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4tr9 A   5 EYMNAPKKLPADVAEELATTAQKLVQAGKGILAADESTQTIKKRFDNIKLENTIENRASYRDLLFGTKGLGKFISGAILFEETLFQKNEAGVPMVNLLHNENIIPGIKVDKGLVNIPCTDEEKSTQGLDGLAERCKEYYKAGARFAKWRTVLVIDTAKGKPTDLSIHETAWGLARYASICQQNRLVPIVEPEILADGPHSIEVCAVVTQKVLSCVFKALQENGVLLEGALLKPNMVTAGYECTAKTTTQDVGFLTVRTLRRTVPPALPGVVFLSGGQSEEEASVNLNSINALGPHPWALTFSYGRALQASVLNTWQGKKENVAKAREVLLQRAEANSLATYGKYKGG 351
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       


Chain B from PDB  Type:PROTEIN  Length:347
                                                                                                                                                                                                                                                                                                                                                                                           
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........hhhhhhhhhhhhhhhh....eeeee..hhhhhhhhhhh.....hhhhhhhhhhhhhh..hhhh.eeeeeehhhhhh.......hhhhhhhhh..eeeee....eee.......eee....hhhhhhhhhhhhh..eeeeeeee.........hhhhhhhhhhhhhhhhhhhhhh..eeeeeeee......hhhhhhhhhhhhhhhhhhhhhhhh.hhhhhee...............hhhhhhhhhhhhhhhhh.....eeee.....hhhhhhhhhhhhhhh.....eeeeeehhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4tr9 B   5 EYMNAPKKLPADVAEELATTAQKLVQAGKGILAADESTQTIKKRFDNIKLENTIENRASYRDLLFGTKGLGKFISGAILFEETLFQKNEAGVPMVNLLHNENIIPGIKVDKGLVNIPCTDEEKSTQGLDGLAERCKEYYKAGARFAKWRTVLVIDTAKGKPTDLSIHETAWGLARYASICQQNRLVPIVEPEILADGPHSIEVCAVVTQKVLSCVFKALQENGVLLEGALLKPNMVTAGYECTAKTTTQDVGFLTVRTLRRTVPPALPGVVFLSGGQSEEEASVNLNSINALGPHPWALTFSYGRALQASVLNTWQGKKENVAKAREVLLQRAEANSLATYGKYKGG 351
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       


Chain C from PDB  Type:PROTEIN  Length:347
                                                                                                                                                                                                                                                                                                                                                                                           
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........hhhhhhhhhhhhhhhh....eeeee....hhhhhhhhh.....hhhhhhhhhhhhhh..hhhh.eeeeeehhhhhh.......hhhhhhhhh..eeeee....eee.......eee....hhhhhhhhhhhhh..eeeeeeee.........hhhhhhhhhhhhhhhhhhhhhh..eeeeeeee......hhhhhhhhhhhhhhhhhhhhhhh..hhhhhee...............hhhhhhhhhhhhhhhhh.....eeee.....hhhhhhhhhhhhhh......eeeeeehhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4tr9 C   5 EYMNAPKKLPADVAEELATTAQKLVQAGKGILAADESTQTIKKRFDNIKLENTIENRASYRDLLFGTKGLGKFISGAILFEETLFQKNEAGVPMVNLLHNENIIPGIKVDKGLVNIPCTDEEKSTQGLDGLAERCKEYYKAGARFAKWRTVLVIDTAKGKPTDLSIHETAWGLARYASICQQNRLVPIVEPEILADGPHSIEVCAVVTQKVLSCVFKALQENGVLLEGALLKPNMVTAGYECTAKTTTQDVGFLTVRTLRRTVPPALPGVVFLSGGQSEEEASVNLNSINALGPHPWALTFSYGRALQASVLNTWQGKKENVAKAREVLLQRAEANSLATYGKYKGG 351
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       


Chain D from PDB  Type:PROTEIN  Length:347
                                                                                                                                                                                                                                                                                                                                                                                           
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........hhhhhhhhhhhhhhhh....eeeee......hhhhhh......hhhhhhhhhhhhhh..hhhh.eeeeeehhhhhh.......hhhhhhhhh..eeeee....eee.......eee....hhhhhhhhhhh....eeeeeeee..hhhhh..hhhhhhhhhhhhhhhhhhhhhh..eeeeeeee......hhhhhhhhhhhhhhhhhhhhhhh..hhhhhee...............hhhhhhhhhhhhhhhhh.....eeee.....hhhhhhhhhhhhhh......eeeeeehhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4tr9 D   5 EYMNAPKKLPADVAEELATTAQKLVQAGKGILAADESTQTIKKRFDNIKLENTIENRASYRDLLFGTKGLGKFISGAILFEETLFQKNEAGVPMVNLLHNENIIPGIKVDKGLVNIPCTDEEKSTQGLDGLAERCKEYYKAGARFAKWRTVLVIDTAKGKPTDLSIHETAWGLARYASICQQNRLVPIVEPEILADGPHSIEVCAVVTQKVLSCVFKALQENGVLLEGALLKPNMVTAGYECTAKTTTQDVGFLTVRTLRRTVPPALPGVVFLSGGQSEEEASVNLNSINALGPHPWALTFSYGRALQASVLNTWQGKKENVAKAREVLLQRAEANSLATYGKYKGG 351
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       


Chain E from PDB  Type:PROTEIN  Length:10
                                          
               SCOP domains ---------- SCOP domains
               CATH domains ---------- CATH domains
               Pfam domains ---------- Pfam domains
         Sec.struct. author ..hhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------- SAPs(SNPs)
                    PROSITE ---------- PROSITE
                 Transcript ---------- Transcript
                 4tr9 E   7 AASLYEKKAA  16
                                    16


Chain G from PDB  Type:PROTEIN  Length:11
                                           
               SCOP domains ----------- SCOP domains
               CATH domains ----------- CATH domains
               Pfam domains ----------- Pfam domains
         Sec.struct. author ...hhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------- SAPs(SNPs)
                    PROSITE ----------- PROSITE
                 Transcript ----------- Transcript
                 4tr9 G   6 AAASLYEKKAA  16
                                    15 


Chain H from PDB  Type:PROTEIN  Length:3
                                   
               SCOP domains --- SCOP domains
               CATH domains --- CATH domains
               Pfam domains --- Pfam domains
         Sec.struct. author ... Sec.struct. author
                 SAPs(SNPs) --- SAPs(SNPs)
                    PROSITE --- PROSITE
                 Transcript --- Transcript
                 4tr9 H 604 DWN 606


Chain I from PDB  Type:PROTEIN  Length:3
                                   
               SCOP domains --- SCOP domains
               CATH domains --- CATH domains
               Pfam domains --- Pfam domains
         Sec.struct. author ... Sec.struct. author
                 SAPs(SNPs) --- SAPs(SNPs)
                    PROSITE --- PROSITE
                 Transcript --- Transcript
                 4tr9 I 604 DWN 606


Chain J from PDB  Type:PROTEIN  Length:3
                                   
               SCOP domains --- SCOP domains
               CATH domains --- CATH domains
               Pfam domains --- Pfam domains
         Sec.struct. author ... Sec.struct. author
                 SAPs(SNPs) --- SAPs(SNPs)
                    PROSITE --- PROSITE
                 Transcript --- Transcript
                 4tr9 J 604 DWN 606


Chain K from PDB  Type:PROTEIN  Length:3
                                   
               SCOP domains --- SCOP domains
               CATH domains --- CATH domains
               Pfam domains --- Pfam domains
         Sec.struct. author ... Sec.struct. author
                 SAPs(SNPs) --- SAPs(SNPs)
                    PROSITE --- PROSITE
                 Transcript --- Transcript
                 4tr9 K 604 DWN 606
   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 4TR9)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4TR9)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4TR9)

(-) Gene Ontology  (11, 12)

Asymmetric/Biological Unit(hide GO term definitions)

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 Related Entries

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

UniProtKB/TrEMBL
        Q76NM2_PLAF7 | Q76NM2: 4hqf 4hqk

(-) Related Entries Specified in the PDB File

2pc4 2PC4 IS THE SAME PROTEIN IN COMPLEX WITH TRAP. THIS NEW SET OF COORDINATES CONTAINS IN ADDITION TO TRAP ALSO AN INHIBITOR.