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(-) Description

Title :  CRYSTAL STRUCTURE OF PLASMODIUM VIVAX LDH IN COMPLEX WITH A DNA APTAMER CALLED PL1
 
Authors :  S. J. Choi, C. Ban
Date :  24 Jan 16  (Deposition) - 19 Oct 16  (Release) - 21 Dec 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.71
Chains :  Asym. Unit :  A,B,C
Biol. Unit 1:  A,B,C  (2x)
Keywords :  Dna Aptamer, Plasmodium Ldh, Malaria, Dna Structural Element, Oxidoreductase-Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. J. Choi, C. Ban
Crystal Structure Of A Dna Aptamer Bound To Pvldh Elucidate Novel Single-Stranded Dna Structural Elements For Folding And Recognition
Sci Rep V. 6 34998 2016
PubMed-ID: 27725738  |  Reference-DOI: 10.1038/SREP34998

(-) Compounds

Molecule 1 - L-LACTATE DEHYDROGENASE
    Chains: A, B
    EC Number: 1.1.1.27
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET28A
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: LDH
    Organism Scientific: PLASMODIUM VIVAX
    Organism Taxid: 5855
    Synonym: LACTATE DEHYDROGENASE,PARASITE LACTATE DEHYDROGENASE
 
Molecule 2 - DNA (32-MER)
    Chains: C
    Engineered: YES
    Organism Scientific: PHYLICA EMIRNENSIS
    Organism Taxid: 178505
    Synthetic: YES

 Structural Features

(-) Chains, Units

  123
Asymmetric Unit : ABC
Biological Unit 1 (2x): ABC

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (1, 1)
No.NameCountTypeFull Name
1MG1Ligand/IonMAGNESIUM ION
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1MG-1Ligand/IonMAGNESIUM ION

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHOH B:435 , DT C:8 , DG C:9 , HOH C:203 , HOH C:238 , HOH C:249binding site for residue MG C 101

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Asn A:127 -Pro A:128
2Asn B:127 -Pro B:128

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5HRU)

(-) 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:305
                                                                                                                                                                                                                                                                                                                                                 
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee..hhhhhhhhhhhhhhh..eeeee....hhhhhhhhhhhhhhhhhh....eeee.hhhhhh...eeee..........hhhhhhhhhhhhhhhhhhhhh...eeee...hhhhhhhhhhhhhh.hhh.eee.hhhhhhhhhhhhhhhhhh.hhh.ee..ee.......ee.hhh.ee..eehhhhhhh...hhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhh...eeeeeeeeee.hhh.eeeeeeeeeeee..eeeee.....hhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5hru A   4 KPKIVLVGSGMIGGVMATLIVQKNLGDVVMFDVVKNMPQGKALDTSHSNVMAYSNCKVTGSNSYDDLKGADVVIVTAGFTKAPRDDLLPLNNKIMIEIGGHIKNLCPNAFIIVVTNPVDVMVQLLFEHSGVPKNKIIGLGGVLDTSRLKYYISQKLNVCPRDVNALIVGAHGNKMVLLKRYITVGGIPLQEFINNKKITDEEVEGIFDRTVNTALEIVNLLASPYVAPAAAIIEMAESYLKDIKKVLVCSTLLEGQYGHSNIFGGTPLVIGGTGVEQVIELQLNAEEKTKFDEAVAETKRMKALI 316
                                    13        23        33        43        53        63        73        83  ||   101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311     
                                                                                                             86|                                                                                                                                                                                                                             
                                                                                                              95                                                                                                                                                                                                                             


Chain B from PDB  Type:PROTEIN  Length:306
                                                                                                                                                                                                                                                                                                                                                  
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...eeeee..hhhhhhhhhhhhhhh..eeeee....hhhhhhhhhhhhhhhhhh....eeee.hhhhhh...eeee.......hhhhhhhhhhhhhhhhhhhhhhhh...eeee...hhhhhhhhhhhhhh.hhh.eee.hhhhhhhhhhhhhhhhhh.hhh.ee..ee.......ee.hhh.ee..eehhhhhhh...hhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhh...eeeeeeeeee.hhh.eeeeeeeeeeee..eeeee.....hhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5hru B   3 PKPKIVLVGSGMIGGVMATLIVQKNLGDVVMFDVVKNMPQGKALDTSHSNVMAYSNCKVTGSNSYDDLKGADVVIVTAGFTKANRDDLLPLNNKIMIEIGGHIKNLCPNAFIIVVTNPVDVMVQLLFEHSGVPKNKIIGLGGVLDTSRLKYYISQKLNVCPRDVNALIVGAHGNKMVLLKRYITVGGIPLQEFINNKKITDEEVEGIFDRTVNTALEIVNLLASPYVAPAAAIIEMAESYLKDIKKVLVCSTLLEGQYGHSNIFGGTPLVIGGTGVEQVIELQLNAEEKTKFDEAVAETKRMKALI 316
                                    12        22        32        42        52        62        72        82  ||   100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310      
                                                                                                             85|                                                                                                                                                                                                                              
                                                                                                              94                                                                                                                                                                                                                              


Chain C from PDB  Type:DNA  Length:32
                                                                
                 5hru C   3 TCGATTGGATTGTGCCGGAAGTGCTGGCTCGA  34
                                    12        22        32
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  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 5HRU)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (8, 8)

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 Related Entries

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        Q4PRK9_PLAVI | Q4PRK9: 2a92 2aa3 5hs4 5hto

(-) Related Entries Specified in the PDB File

5hs4 5hto