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(-) Description

Title :  CRYSTAL STRUCTURE OF PLASMODIUM VIVAX LDH IN COMPLEX WITH A DNA APTAMER CALLED PL1 (TETRAMERIC LDH IN AN ASYMMETRIC UNIT)
 
Authors :  S. J. Choi, C. Ban
Date :  27 Jan 16  (Deposition) - 19 Oct 16  (Release) - 21 Dec 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym./Biol. Unit :  A,B,C,D,E,F
Keywords :  Ldh, Malaria, Dna Aptamer, Aptamer, 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, D, E
    EC Number: 1.1.1.27
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: ER2566
    Expression System Taxid: 562
    Gene: LDH
    Organism Scientific: PLASMODIUM VIVAX
    Organism Taxid: 5855
    Synonym: LACTATE DEHYDROGENASE,PARASITE LACTATE DEHYDROGENASE
 
Molecule 2 - DNA (34-MER)
    Chains: C
    Engineered: YES
    Organism Scientific: PLASMODIUM VIVAX
    Organism Taxid: 5855
    Synthetic: YES
 
Molecule 3 - DNA (30-MER)
    Chains: F
    Engineered: YES
    Organism Scientific: PLASMODIUM VIVAX
    Organism Taxid: 5855
    Synthetic: YES

 Structural Features

(-) Chains, Units

  123456
Asymmetric/Biological Unit : ABCDEF

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric/Biological Unit (1, 2)
No.NameCountTypeFull Name
1MG2Ligand/IonMAGNESIUM ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREDT C:8 , DG C:9 , HOH C:211 , HOH C:242 , HOH C:243 , HOH C:248binding site for residue MG C 101
2AC2SOFTWAREDT F:8 , DG F:9 , HOH F:203 , HOH F:213 , HOH F:227 , HOH F:229binding site for residue MG F 101

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1Asn A:127 -Pro A:128
2Asn B:127 -Pro B:128
3Asn D:127 -Pro D:128
4Asn E:127 -Pro E:128

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5HTO)

(-) 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:302
                                                                                                                                                                                                                                                                                                                                              
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee..hhhhhhhhhhhhhhh..eeeee....hhhhhhhhhhhhhhhhhh....eeee.hhhhhh...eeee.........hhhhhhhhhhhhhhhhhhh...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
                 5hto A   4 KPKIVLVGSGMIGGVMATLIVQKNLGDVVMFDVVKNMPQGKALDTSHSNVMAYSNCKVTGSNSYDDLKGADVVIVTAGFTKAPLLPLNNKIMIEIGGHIKNLCPNAFIIVVTNPVDVMVQLLFEHSGVPKNKIIGLGGVLDTSRLKYYISQKLNVCPRDVNALIVGAHGNKMVLLKRYITVGGIPLQEFINNKKITDEEVEGIFDRTVNTALEIVNLLASPYVAPAAAIIEMAESYLKDIKKVLVCSTLLEGQYGHSNIFGGTPLVIGGTGVEQVIELQLNAEEKTKFDEAVAETKRMKALI 316
                                    13        23        33        43        53        63        73        83  ||   104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314  
                                                                                                             86|                                                                                                                                                                                                                          
                                                                                                              98                                                                                                                                                                                                                          


Chain B from PDB  Type:PROTEIN  Length:303
                                                                                                                                                                                                                                                                                                                                               
               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
                 5hto B   4 KPKIVLVGSGMIGGVMATLIVQKNLGDVVMFDVVKNMPQGKALDTSHSNVMAYSNCKVTGSNSYDDLKGADVVIVTAGFTKRDDLLPLNNKIMIEIGGHIKNLCPNAFIIVVTNPVDVMVQLLFEHSGVPKNKIIGLGGVLDTSRLKYYISQKLNVCPRDVNALIVGAHGNKMVLLKRYITVGGIPLQEFINNKKITDEEVEGIFDRTVNTALEIVNLLASPYVAPAAAIIEMAESYLKDIKKVLVCSTLLEGQYGHSNIFGGTPLVIGGTGVEQVIELQLNAEEKTKFDEAVAETKRMKALI 316
                                    13        23        33        43        53        63        73        83||     103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313   
                                                                                                           84|                                                                                                                                                                                                                             
                                                                                                            95                                                                                                                                                                                                                             


Chain C from PDB  Type:DNA  Length:34
                                                                  
                 5hto C   2 TTCGATTGGATTGTGCCGGAAGTGCTGGCTCGAA  35
                                    11        21        31    


Chain D from PDB  Type:PROTEIN  Length:304
                                                                                                                                                                                                                                                                                                                                                
               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
                 5hto D   4 KPKIVLVGSGMIGGVMATLIVQKNLGDVVMFDVVKNMPQGKALDTSHSNVMAYSNCKVTGSNSYDDLKGADVVIVTAGFTKAPDDLLPLNNKIMIEIGGHIKNLCPNAFIIVVTNPVDVMVQLLFEHSGVPKNKIIGLGGVLDTSRLKYYISQKLNVCPRDVNALIVGAHGNKMVLLKRYITVGGIPLQEFINNKKITDEEVEGIFDRTVNTALEIVNLLASPYVAPAAAIIEMAESYLKDIKKVLVCSTLLEGQYGHSNIFGGTPLVIGGTGVEQVIELQLNAEEKTKFDEAVAETKRMKALI 316
                                    13        23        33        43        53        63        73        83  ||   102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312    
                                                                                                             86|                                                                                                                                                                                                                            
                                                                                                              96                                                                                                                                                                                                                            


Chain E 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
                 5hto E   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 F from PDB  Type:DNA  Length:30
                                                              
                 5hto F   4 CGATTGGATTGTGCCGGAAGTGCTGGCTCG  33
                                    13        23        33
   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 5HTO)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (8, 8)

Asymmetric/Biological Unit(hide GO term definitions)

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

(-) Related Entries Specified in the PDB File

5hru 5hs4