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(-) Description

Title :  CRYSTAL STRUCTURE OF PLASMODIUM DXR IN COMPLEX WITH A PYRIDINE-CONTAINING INHIBITOR
 
Authors :  J. Diao, J. Xue, G. Cai, L. Deng, Y. Song
Date :  25 Jul 12  (Deposition) - 06 Feb 13  (Release) - 10 Jul 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Nadph Binding, Isomerase-Isomerase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. Xue, J. Diao, G. Cai, L. Deng, B. Zheng, Y. Yao, Y. Song
Antimalarial And Structural Studies Of Pyridine-Containing Inhibitors Of 1-Deoxyxylulose-5-Phosphate Reductoisomerase.
Acs Med Chem Lett V. 4 278 2013
PubMed-ID: 23795240  |  Reference-DOI: 10.1021/ML300419R

(-) 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: PQE30
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: DXR
    Mutation: YES
    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  (7, 16)

Asymmetric/Biological Unit (7, 16)
No.NameCountTypeFull Name
1ACT2Ligand/IonACETATE ION
2CL1Ligand/IonCHLORIDE ION
3EDO3Ligand/Ion1,2-ETHANEDIOL
4FOB2Ligand/Ion[(1R)-3-[ACETYL(HYDROXY)AMINO]-1-(PYRIDIN-4-YL)PROPYL]PHOSPHONIC ACID
5FOQ2Ligand/Ion[(1S)-3-[ACETYL(HYDROXY)AMINO]-1-(PYRIDIN-4-YL)PROPYL]PHOSPHONIC ACID
6MN4Ligand/IonMANGANESE (II) ION
7NDP2Ligand/IonNADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDEPHOSPHATE

(-) Sites  (16, 16)

Asymmetric Unit (16, 16)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREGLY 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 , LYS A:205 , GLU A:206 , ASP A:231 , TRP A:296 , MET A:298 , GLY A:299 , MET A:360 , HOH A:1552 , HOH A:1560BINDING SITE FOR RESIDUE NDP A 501
02AC2SOFTWAREASP 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 , CYS A:338 , NDP A:501 , MN A:504 , HOH A:1516 , HOH A:1523BINDING SITE FOR RESIDUE FOB A 502
03AC3SOFTWAREASP 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 , CYS A:338 , NDP A:501 , MN A:504 , HOH A:1516BINDING SITE FOR RESIDUE FOQ A 503
04AC4SOFTWAREASP A:231 , GLU A:233 , GLU A:315BINDING SITE FOR RESIDUE MN A 504
05AC5SOFTWARELYS A:245 , ASN A:261BINDING SITE FOR RESIDUE CL A 505
06AC6SOFTWARETYR A:357BINDING SITE FOR RESIDUE ACT A 506
07AC7SOFTWAREASP A:324BINDING SITE FOR RESIDUE EDO A 507
08AC8SOFTWAREGLY B:84 , THR B:86 , GLY B:87 , SER B:88 , ILE B:89 , TYR B:113 , VAL B:114 , ASN B:115 , LYS B:116 , SER B:117 , HIS B:136 , GLY B:180 , ILE B:181 , ASP B:182 , GLN B:185 , ALA B:203 , ASN B:204 , LYS B:205 , GLU B:206 , ASP B:231 , TRP B:296 , GLY B:299 , MET B:360 , HOH B:628 , HOH B:657BINDING SITE FOR RESIDUE NDP B 501
09AC9SOFTWARELYS B:205 , ASP B:231 , SER B:232 , GLU B:233 , SER B:269 , SER B:270 , TRP B:296 , MET B:298 , SER B:306 , ASN B:311 , LYS B:312 , GLU B:315 , CYS B:338 , NDP B:501 , MN B:504 , HOH B:602 , HOH B:626BINDING SITE FOR RESIDUE FOB B 502
10BC1SOFTWARELYS B:205 , ASP B:231 , SER B:232 , GLU B:233 , SER B:269 , SER B:270 , TRP B:296 , MET B:298 , SER B:306 , ASN B:311 , LYS B:312 , GLU B:315 , CYS B:338 , MN B:504 , HOH B:626BINDING SITE FOR RESIDUE FOQ B 503
11BC2SOFTWARELYS B:205 , ASP B:231 , GLU B:233 , GLU B:315BINDING SITE FOR RESIDUE MN B 504
12BC3SOFTWAREASP A:242 , HOH A:1514 , HOH A:1542 , GLN B:239 , LEU B:241 , HOH B:623 , HOH B:654BINDING SITE FOR RESIDUE MN B 505
13BC4SOFTWAREASN B:452 , HOH B:615BINDING SITE FOR RESIDUE MN B 506
14BC5SOFTWAREGLN B:454 , HOH B:647BINDING SITE FOR RESIDUE ACT B 507
15BC6SOFTWARESER B:441 , SER B:445BINDING SITE FOR RESIDUE EDO B 508
16BC7SOFTWAREPRO B:371 , ASP B:372BINDING SITE FOR RESIDUE EDO B 509

(-) SS Bonds  (0, 0)

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

(-) 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 4GAE)

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4GAE)

(-) 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:416
                                                                                                                                                                                                                                                                                                                                                                                                                                                                
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eeeeee...hhhhhhhhhhhhhhh.....eeeeeeee..hhhhhhhhhhhhh..eeee.hhhhhhhhhhhhhh......eeeehhhhhhhhhh.....eeee...hhhhhhhhhhhhhh..eeee..hhhhhhhhhhhhhhhhhh...eeee.hhhhhhhhhh.hhhhhh.......hhhhhh.eeeeeeee........hhhhhhh.hhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhh.hhh.eeeee.....eeeeeee....eeeee....hhhhhhhhhhh...........hhhhhheee........hhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4gae A  71 HHGSKKPINVAIFGSTGSIGTNALNIIRECNKIENVFNVKALYVNKSVNELYEQAREFLPEYLCIHDKSVYEELKELVKNIKDYKPIILCGDEGMKEICSSNSIDKIVIGIDSFQGLYSTMYAIMNNKIVALANKESIVSAGFFLKKLLNIHKNAKIIPVDSEHSAIFQCLDNNKVIKTKCLQDNFSKINNINKIFLCSSGGPFQNLTMDELKNVTSENALKHPKWKMGKKITIDSATMMNKGLEVIETHFLFDVDYNDIEVIVHKECIIHSCVEFIDKSVISQMYYPDMQIPILYSLTWPDRIKTNLKPLDLAQVSTLTFHKPSLEHFPCIKLAYQAGIKGNFYPTVLNASNEIANNLFLNNKIKYFDISSIISQVLESFNSQKVSENSEDLMKQILQIHSWAKDKATDIYNKHN 486
                                    80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450       460       470       480      


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...hhhhhhhhhhhhhh..eeee.hhhhhhhhhhhhhhhhhhh...eeee.hhhhhhhhhhhhhhhhh.......hhhhhh.eeeeeeee........hhhhhhh.hhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhh.hhh.eeeee.....eeeeeee....eeeee....hhhhhhhhhhh...........hhhhhheee........hhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4gae B  77 PINVAIFGSTGSIGTNALNIIRECNKIENVFNVKALYVNKSVNELYEQAREFLPEYLCIHDKSVYEELKELVKNIKDYKPIILCGDEGMKEICSSNSIDKIVIGIDSFQGLYSTMYAIMNNKIVALANKESIVSAGFFLKKLLNIHKNAKIIPVDSEHSAIFQCLDNNKVIKTKCLQDNFSKINNINKIFLCSSGGPFQNLTMDELKNVTSENALKHPKWKMGKKITIDSATMMNKGLEVIETHFLFDVDYNDIEVIVHKECIIHSCVEFIDKSVISQMYYPDMQIPILYSLTWPDRIKTNLKPLDLAQVSTLTFHKPSLEHFPCIKLAYQAGIKGNFYPTVLNASNEIANNLFLNNKIKYFDISSIISQVLESFNSQKVSENSEDLMKQILQIHSWAKDKATDIYNKHN 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 4GAE)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (9, 9)

Asymmetric/Biological Unit(hide GO term definitions)

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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 4kp7

(-) Related Entries Specified in the PDB File

3au9 THE SAME PROTEIN COMPLEXED WITH FOSMIDOMYCIN