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(-) Description

Title :  STRUCTURE OF PLASMODIUM FALCIPARUM DXR IN COMPLEX WITH A BETA-SUBSTITUTED FOSMIDOMYCIN ANALOGUE, LC52 AND MANGANESE
 
Authors :  S. Sooriyaarachchi, T. Bergfors, T. A. Jones, S. L. Mowbray
Date :  13 Apr 16  (Deposition) - 24 Aug 16  (Release) - 28 Sep 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.70
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Enzyme-Inhibitor Complex, Mep Pathway, Isoprenoid Biosynthesis, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. Sooriyaarachchi, R. Chofor, M. D. Risseeuw, T. Bergfors, J. Pouyez C. S. Dowd, L. Maes, J. Wouters, T. A. Jones, S. Van Calenbergh, S. L. Mowbray
Targeting An Aromatic Hotspot In Plasmodium Falciparum 1-Deoxy-D-Xylulose-5-Phosphate Reductoisomerase With Beta-Arylpropyl Analogues Of Fosmidomycin.
Chemmedchem V. 11 2024 2016
PubMed-ID: 27487410  |  Reference-DOI: 10.1002/CMDC.201600249
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - 1-DEOXY-D-XYLULOSE 5-PHOSPHATE REDUCTOISOMERASE, APICOPLASTIC
    Chains: A, B
    EC Number: 1.1.1.267
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PEXP5-CT/TOPO
    Expression System Taxid: 469008
    Expression System Variant: C43
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 75-488
    Gene: DXR, PF14_0641
    Organ: APICOPLAST
    Organism Scientific: PLASMODIUM FALCIPARUM (ISOLATE 3D7)
    Organism Taxid: 36329
    Other Details: MATURE PROTEIN LACKS SIGNAL AND APICOPLAST TARGETING SEQUENCES
    Synonym: DXP REDUCTOISOMERASE

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 20)

Asymmetric/Biological Unit (4, 20)
No.NameCountTypeFull Name
16J82Ligand/Ion[(2R)-2-{2-[HYDROXY(METHYL)AMINO]-2-OXOETHYL}-5-(4-METHOXYPHENYL)PENTYL]PHOSPHONIC ACID
2EDO15Ligand/Ion1,2-ETHANEDIOL
3GOL1Ligand/IonGLYCEROL
4MN2Ligand/IonMANGANESE (II) ION

(-) Sites  (20, 20)

Asymmetric Unit (20, 20)
No.NameEvidenceResiduesDescription
01AC1SOFTWARELYS A:205 , ASP A:231 , SER A:232 , GLU A:233 , SER A:269 , SER A:270 , TRP A:296 , SER A:306 , ASN A:311 , LYS A:312 , GLU A:315 , HIS A:341 , PRO A:358 , ASP A:359 , MN A:502 , HOH A:609 , HOH A:612binding site for residue 6J8 A 501
02AC2SOFTWARELYS A:205 , ASP A:231 , GLU A:233 , GLU A:315 , 6J8 A:501binding site for residue MN A 502
03AC3SOFTWARESER A:232 , GLU A:233 , SER A:269 , SER A:270 , HIS A:335 , CYS A:338 , ILE A:340 , HIS A:341binding site for residue GOL A 503
04AC4SOFTWAREVAL A:332 , TYR A:406 , EDO A:508 , HOH A:642binding site for residue EDO A 504
05AC5SOFTWAREASP A:326 , TYR A:327 , ASN A:328binding site for residue EDO A 505
06AC6SOFTWAREILE A:262 , ASN A:263 , ASP A:326 , ASP A:329 , HOH A:749binding site for residue EDO A 506
07AC7SOFTWAREVAL A:209 , SER A:210 , ALA A:211 , GLY A:212 , PHE A:213 , ASN A:413 , PHE A:414 , PRO A:416 , THR A:417binding site for residue EDO A 507
08AC8SOFTWARELYS A:403 , TYR A:406 , EDO A:504 , HOH A:632 , HOH A:687binding site for residue EDO A 508
09AC9SOFTWAREGLN A:446 , HIS A:485binding site for residue EDO A 509
10AD1SOFTWAREASN A:276 , HIS A:398 , GLU A:461 , HOH A:773binding site for residue EDO A 510
11AD2SOFTWARELYS B:205 , ASP B:231 , SER B:232 , GLU B:233 , SER B:269 , SER B:270 , TRP B:296 , SER B:306 , ASN B:311 , LYS B:312 , GLU B:315 , HIS B:341 , PRO B:358 , ASP B:359 , MET B:360 , MN B:502 , HOH B:608 , HOH B:615 , HOH B:623binding site for residue 6J8 B 501
12AD3SOFTWARELYS B:205 , ASP B:231 , GLU B:233 , GLU B:315 , 6J8 B:501binding site for residue MN B 502
13AD4SOFTWAREVAL B:209 , SER B:210 , ALA B:211 , GLY B:212 , PHE B:213 , ASN B:413 , PHE B:414 , PRO B:416 , THR B:417binding site for residue EDO B 503
14AD5SOFTWAREGLU B:331 , VAL B:332 , TYR B:406 , HOH B:699binding site for residue EDO B 504
15AD6SOFTWAREILE B:262 , ASN B:263 , VAL B:325 , ASP B:326 , ASP B:329binding site for residue EDO B 505
16AD7SOFTWAREGLN A:239 , LEU A:241 , ASP A:242 , HOH A:603 , GLN B:239 , LEU B:241 , ASP B:242 , HOH B:612 , HOH B:618 , HOH B:620binding site for residue EDO B 506
17AD8SOFTWARELYS A:102 , ILE A:103 , LYS B:102 , ILE B:103binding site for residue EDO B 507
18AD9SOFTWARELYS B:223 , LYS B:434 , LYS B:436 , HOH B:609 , HOH B:667binding site for residue EDO B 508
19AE1SOFTWAREGLY B:180 , HOH B:603 , HOH B:765binding site for residue EDO B 509
20AE2SOFTWARETHR B:249 , GLN B:253 , ASN B:284 , THR B:286 , ASN B:289 , HOH B:622binding site for residue EDO B 510

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Trp A:370 -Pro A:371
2Trp B:370 -Pro B:371

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5JBI)

(-) 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:410
                                                                                                                                                                                                                                                                                                                                                                                                                                                          
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee...hhhhhhhhhhhhhhhhhh..eeeeeeee..hhhhhhhhhhhhh..eeee.hhhhhhhhhhhhh.......eeeehhhhhhhhhhh....eeee..hhhhhhhhhhhhhhh..eeee.hhhhhhhhhhhhhhhhhhh...eeee.hhhhhhhhhh.hhhhhh.......hhhhhh.eeeeeeee........hhhhhhh.hhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhh.hhh.eeeee.....eeeeeee....eeeee....hhhhhhhhhhh...........hhhhhheee........hhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5jbi A  77 PINVAIFGSTGSIGTNALNIIRECNKIENVFNVKALYVNKSVNELYEQAREFLPEYLCIHDKSVYEELKELVKNIKDYKPIILCGDEGMKEICSSNSIDKIVIGIDSFQGLYSTMYAIMNNKIVALANKESIVSAGFFLKKLLNIHKNAKIIPVDSEHSAIFQCLDNNKVLKTKCLQDNFSKINNINKIFLCSSGGPFQNLTMDELKNVTSENALKHPKWKMGKKITIDSATMMNKGLEVIETHFLFDVDYNDIEVIVHKECIIHSCVEFIDKSVISQMYYPDMQIPILYSLTWPDRIKTNLKPLDLAQVSTLTFHKPSLEHFPCIKLAYQAGIKGNFYPTVLNASNEIANNLFLNNKIKYFDISSIISQVLESFNSQKVSENSEDLMKQILQIHSWAKDKATDIYNKHN 486
                                    86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       356       366       376       386       396       406       416       426       436       446       456       466       476       486


Chain B from PDB  Type:PROTEIN  Length:410
                                                                                                                                                                                                                                                                                                                                                                                                                                                          
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee...hhhhhhhhhhhhhhhhhh..eeeeeeee..hhhhhhhhhhhhh..eeee.hhhhhhhhhhhhh.......eeeehhhhhhhhhh.....eeee..hhhhhhhhhhhhhhh..eeee.hhhhhhhhhhhhhhhhhhh...eeee.hhhhhhhhhh.hhhhhh.......hhhhhh.eeeeeeee........hhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhh.hhh.eeeee.....eeeeeee....eeeee....hhhhhhhhhhh...........hhhhhheee........hhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5jbi B  77 PINVAIFGSTGSIGTNALNIIRECNKIENVFNVKALYVNKSVNELYEQAREFLPEYLCIHDKSVYEELKELVKNIKDYKPIILCGDEGMKEICSSNSIDKIVIGIDSFQGLYSTMYAIMNNKIVALANKESIVSAGFFLKKLLNIHKNAKIIPVDSEHSAIFQCLDNNKVLKTKCLQDNFSKINNINKIFLCSSGGPFQNLTMDELKNVTSENALKHPKWKMGKKITIDSATMMNKGLEVIETHFLFDVDYNDIEVIVHKECIIHSCVEFIDKSVISQMYYPDMQIPILYSLTWPDRIKTNLKPLDLAQVSTLTFHKPSLEHFPCIKLAYQAGIKGNFYPTVLNASNEIANNLFLNNKIKYFDISSIISQVLESFNSQKVSENSEDLMKQILQIHSWAKDKATDIYNKHN 486
                                    86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       356       366       376       386       396       406       416       426       436       446       456       466       476       486
   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 5JBI)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (11, 11)

Asymmetric/Biological Unit(hide GO term definitions)

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        DXR_PLAF7 | Q8IKG4: 4y67 4y6p 4y6r 4y6s 5jaz 5jc1 5jmp 5jmw 5jnl 5jo0

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