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(-) Description

Title :  STRUCTURE OF PLASMODIUM ISPC IN COMPLEX WITH A BETA-THIA-ISOSTERE DERIVATIVE OF FOSMIDOMYCIN
 
Authors :  A. Kunfermann, A. Bacher, M. Groll
Date :  13 May 13  (Deposition) - 02 Oct 13  (Release) - 12 Feb 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Dxp Pathway, Drug Optimization, Non-Covalent Inhibition, Malaria, Tuberculosis, Rossmann Fold, Reductoisomerase, Nadph Binding, Apicoplast, Oxidoreductase-Oxidoreductase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. Kunfermann, C. Lienau, B. Illarionov, J. Held, T. Grawert, C. T. Behrendt, P. Werner, S. Hahn, W. Eisenreich, U. Riederer, B. Mordmuller, A. Bacher, M. Fischer, M. Groll, T. Kurz
Ispc As Target For Antiinfective Drug Discovery: Synthesis, Enantiomeric Separation, And Structural Biology Of Fosmidomycin Thia Isosters.
J. Med. Chem. V. 56 8151 2013
PubMed-ID: 24032981  |  Reference-DOI: 10.1021/JM4012559

(-) Compounds

Molecule 1 - 1-DEOXY-D-XYLULOSE 5-PHOSPHATE REDUCTOISOMERASE, APICOPLAST
    Chains: A, B
    EC Number: 1.1.1.267
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PQEISPCPLASART
    Expression System Strain: M15 PREP4
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: CODON OPTIMIZED FORM, DXR, SYNTHETIC
    Organism Scientific: PLASMODIUM FALCIPARUM
    Organism Taxid: 137071
    Synonym: 1-DEOXYXYLULOSE-5-PHOSPHATE REDUCTOISOMERASE, DOXP REDUCTOISOMERASE, DXP REDUCTOISOMERASE

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 5)

Asymmetric/Biological Unit (3, 5)
No.NameCountTypeFull Name
11UQ2Ligand/Ion[(S)-({2-[HYDROXY(METHYL)AMINO]-2-OXOETHYL}SULFANYL)(PHENYL)METHYL]PHOSPHONIC ACID
2MN32Ligand/IonMANGANESE (III) ION
3NAP1Ligand/IonNADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELYS A:205 , ASP A:231 , GLU A:233 , GLU A:315 , 1UQ A:503BINDING SITE FOR RESIDUE MN3 A 501
2AC2SOFTWAREGLY A:84 , THR A:86 , GLY A:87 , SER A:88 , ILE A:89 , TYR A:113 , VAL A:114 , ASN A:115 , LYS A:116 , SER A:117 , HIS A:136 , GLY A:180 , ILE A:181 , ASP A:182 , GLN A:185 , ALA A:203 , ASN A:204 , GLU A:206 , ASP A:231 , TRP A:296 , GLY A:299 , ILE A:302 , MET A:360 , HOH A:613 , HOH A:631BINDING SITE FOR RESIDUE NAP A 502
3AC3SOFTWARELYS A:205 , ASP A:231 , SER A:232 , GLU A:233 , SER A:269 , SER A:270 , TRP A:296 , MET A:298 , SER A:306 , ASN A:311 , LYS A:312 , GLU A:315 , MN3 A:501 , HOH A:619 , HOH A:627BINDING SITE FOR RESIDUE 1UQ A 503
4AC4SOFTWARELYS B:205 , ASP B:231 , GLU B:233 , GLU B:315 , 1UQ B:502BINDING SITE FOR RESIDUE MN3 B 501
5AC5SOFTWARELYS B:205 , ASP B:231 , SER B:232 , GLU B:233 , SER B:269 , SER B:270 , MET B:298 , SER B:306 , ASN B:311 , LYS B:312 , GLU B:315 , MN3 B:501 , HOH B:638 , HOH B:654BINDING SITE FOR RESIDUE 1UQ B 502

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4KP7)

(-) 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 4KP7)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4KP7)

(-) Exons   (0, 0)

(no "Exon" information available for 4KP7)

(-) 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:409
                                                                                                                                                                                                                                                                                                                                                                                                                                                         
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee...hhhhhhhhhhhhhhhhhh..eeeeeeee..hhhhhhhhhhhhh..eeee.hhhhhhhhhhhhhhh.....eeeehhhhhhhhhhh....eeee...hhhhhhhhhhhhhh..eeee.hhhhhhhhhhhhhhhhhhh...eeee.hhhhhhhhhh.hhhhhh.......hhhhhh.eeeeeeee........hhhhhh..hhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhh.hhh.eeeee.....eeeeeee....eeeee....hhhhhhhhhhh...........hhhhhheee........hhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4kp7 A  77 PINVAIFGSTGSIGTNALNIIRECNKIENVFNVKALYVNKSVNELYEQAREFLPEYLCIHDKSVYEELKELVKNIKDYKPIILCGDEGMKEICSSNSIDKIVIGIDSFQGLYSTMYAIMNNKIVALANKESIVSAGFFLKKLLNIHKNAKIIPVDSEHSAIFQCLDNNKVLKTKCLQDNFSKINNINKIFLCSSGGPFQNLTMDELKNVTSENALKHPKWKMGKKITIDSATMMNKGLEVIETHFLFDVDYNDIEVIVHKECIIHSCVEFIDKSVISQMYYPDMQIPILYSLTWPDRIKTNLKPLDLAQVSTLTFHKPSLEHFPCIKLAYQAGIKGNFYPTVLNASNEIANNLFLNNKIKYFDISSIISQVLESFNSQKVSENSEDLMKQILQIHSWAKDKATDIYNKH 485
                                    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         


Chain B from PDB  Type:PROTEIN  Length:402
                                                                                                                                                                                                                                                                                                                                                                                                                                                  
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeeee...hhhhhhhhhhhhhhhhhh..eeeeeeee..hhhhhhhhhhhhh..eeee.hhhhhhhhhhhhh.......eeeehhhhhhhhhhh....eeee...hhhhhhhhhhhhhh..eeee.hhhhhhhhhhhhhhhhhhh...eeee.hhhhhhhhhh.hhhhhh.......hhhhhh.eeeeeeee........hhhhhh..hhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhh.hhh.eeeee.....eeeeeee....eeeee....hhhhhhhhhhh...........hhhhhheee........hhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4kp7 B  77 PINVAIFGSTGSIGTNALNIIRECNKIENVFNVKALYVNKSVNELYEQAREFLPEYLCIHDKSVYEELKELVKNIKDYKPIILCGDEGMKEICSSNSIDKIVIGIDSFQGLYSTMYAIMNNKIVALANKESIVSAGFFLKKLLNIHKNAKIIPVDSEHSAIFQCLDNNKVLKTKCLQDNFSKINNINKIFLCSSGGPFQNLTMDELKNVTSENALMGKKITIDSATMMNKGLEVIETHFLFDVDYNDIEVIVHKECIIHSCVEFIDKSVISQMYYPDMQIPILYSLTWPDRIKTNLKPLDLAQVSTLTFHKPSLEHFPCIKLAYQAGIKGNFYPTVLNASNEIANNLFLNNKIKYFDISSIISQVLESFNSQKVSENSEDLMKQILQIHSWAKDKATDIYNK 484
                                    86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286    || 302       312       322       332       342       352       362       372       382       392       402       412       422       432       442       452       462       472       482  
                                                                                                                                                                                                                                                291|                                                                                                                                                                                          
                                                                                                                                                                                                                                                 298
   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 4KP7)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4KP7)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4KP7)

(-) Gene Ontology  (9, 9)

Asymmetric/Biological Unit(hide GO term definitions)

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    Trp A:370 - Pro A:371   [ RasMol ]  
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 Related Entries

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

UniProtKB/Swiss-Prot
        DXR_PLAFX | O96693: 3au8 3au9 3aua 3wqq 3wqr 3wqs 4gae

(-) Related Entries Specified in the PDB File

3au8 APO ISPC
3au9 ISPC:FOM-COMPLEX