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(-) Description

Title :  CRYSTAL STRUCTURE OF PLASMODIUM VIVAX PRX1A
 
Authors :  M. C. Gretes, P. A. Karplus
Date :  01 Jun 13  (Deposition) - 09 Nov 16  (Release) - 09 Nov 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.50
Chains :  Asym./Biol. Unit :  A,B,C,D,E,F,G,H,I,J
Keywords :  Oxidoreductase, Peroxiredoxin, Disulfide, Antioxidant, Malaria Parasite (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. C. Gretes, P. A. Karplus
Observed Octameric Assembly Of A Plasmodium Yoelii Peroxiredoxin Can Be Explained By The Replacement Of Native "Ball-And-Socket" Interacting Residues By An Affinity Tag.
Protein Sci. V. 22 1445 2013
PubMed-ID: 23934758  |  Reference-DOI: 10.1002/PRO.2328
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - 2-CYS PEROXIREDOXIN, PUTATIVE
    Chains: A, B, C, D, E, F, G, H, I, J
    EC Number: 1.11.1.15
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET28 LIC/TEV DER
    Expression System Strain: BL21CODONPLUS/RIL
    Expression System Taxid: 511693
    Expression System Vector Type: PLASMID
    Gene: PVX_118545
    Organism Common: APICOMPLEXANS
    Organism Scientific: PLASMODIUM VIVAX SAL-1
    Organism Taxid: 126793
    Strain: SAI-1

 Structural Features

(-) Chains, Units

  12345678910
Asymmetric/Biological Unit : ABCDEFGHIJ

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (1, 2)
No.NameCountTypeFull Name
1ACT2Ligand/IonACETATE ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETYR A:42 , VAL A:49 , CYS A:50 , ILE A:54 , ARG A:125 , HOH A:317BINDING SITE FOR RESIDUE ACT A 201
2AC2SOFTWAREPHE C:41BINDING SITE FOR RESIDUE ACT C 201

(-) SS Bonds  (5, 5)

Asymmetric/Biological Unit
No.Residues
1A:50 -B:170
2C:50 -D:170
3G:170 -H:50
4I:50 -J:170
5I:170 -J:50

(-) Cis Peptide Bonds  (3, 3)

Asymmetric/Biological Unit
No.Residues
1Cys D:170 -Pro D:171
2Pro D:171 -Ala D:172
3Ile I:146 -Gly I:147

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4L0U)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4L0U)

(-) Exons   (0, 0)

(no "Exon" information available for 4L0U)

(-) 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:168
                                                                                                                                                                                                        
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...........eeeee.....eeeee.hhh....eeeeee........hhhhhhhhhhhhhhhhhh.eeeeeee..hhhhhhhhhh.hhhhh.......eeee...hhhhhhh..ee...ee.eeeeee.....eeeeeee......hhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4l0u A   2 PTYVGKEAPFFKAEAVFGDNSFGEVNLTQFIGKKYVLLYFYPLDFTFVCPSEIIALDKALDAFHERNVELLGCSVDSKYTHLAWKKTPLAKGGIGNIKHTLLSDITKSISKDYNVLFDDSVSLRAFVLIDMNGIVQHLLVNNLAIGRSVDEILRIIDAIQHHEKYGDV 169
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161        


Chain B from PDB  Type:PROTEIN  Length:171
                                                                                                                                                                                                           
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...........eeeee.....eeeee.hhh....eeeeee.........hhhhhhhhhhhhhhhhh.eeeeeee..hhhhhhhhhh.hhhhh.......eeee...hhhhhhh..ee...ee.eeeeee.....eeeeeee......hhhhhhhhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4l0u B   2 PTYVGKEAPFFKAEAVFGDNSFGEVNLTQFIGKKYVLLYFYPLDFTFVCPSEIIALDKALDAFHERNVELLGCSVDSKYTHLAWKKTPLAKGGIGNIKHTLLSDITKSISKDYNVLFDDSVSLRAFVLIDMNGIVQHLLVNNLAIGRSVDEILRIIDAIQHHEKYGDVCPA 172
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171 


Chain C from PDB  Type:PROTEIN  Length:172
                                                                                                                                                                                                            
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ............eeeee.....eeeee.hhh....eeeeee.........hhhhhhhhhhhhhhhhh.eeeeeee..hhhhhhhhhh.hhhhh.......eeee...hhhhhhh..ee...ee.eeeeee.....eeeeeee......hhhhhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4l0u C   1 SPTYVGKEAPFFKAEAVFGDNSFGEVNLTQFIGKKYVLLYFYPLDFTFVCPSEIIALDKALDAFHERNVELLGCSVDSKYTHLAWKKTPLAKGGIGNIKHTLLSDITKSISKDYNVLFDDSVSLRAFVLIDMNGIVQHLLVNNLAIGRSVDEILRIIDAIQHHEKYGDVCPA 172
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170  


Chain D from PDB  Type:PROTEIN  Length:171
                                                                                                                                                                                                           
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...........eeeee.....eeeee.hhhh...eeeeee.........hhhhhhhhhhhhhhhhh.eeeeeee..hhhhhhhhhh.hhhhh.......eeee...hhhhhhh..ee...ee.eeeeee.....eeeeeee......hhhhhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4l0u D   2 PTYVGKEAPFFKAEAVFGDNSFGEVNLTQFIGKKYVLLYFYPLDFTFVCPSEIIALDKALDAFHERNVELLGCSVDSKYTHLAWKKTPLAKGGIGNIKHTLLSDITKSISKDYNVLFDDSVSLRAFVLIDMNGIVQHLLVNNLAIGRSVDEILRIIDAIQHHEKYGDVCPA 172
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171 


Chain E from PDB  Type:PROTEIN  Length:162
                                                                                                                                                                                                  
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...........eeeee.....eeeee.hhh....eeeeee.........hhhhhhhhhhhhhhhhh.eeeeeee..hhhhhhhhhh.hhhhh.......eeee...hhhhhhh..ee...ee.eeeeee.....eeeeeee......hhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4l0u E   2 PTYVGKEAPFFKAEAVFGDNSFGEVNLTQFIGKKYVLLYFYPLDFTFVCPSEIIALDKALDAFHERNVELLGCSVDSKYTHLAWKKTPLAKGGIGNIKHTLLSDITKSISKDYNVLFDDSVSLRAFVLIDMNGIVQHLLVNNLAIGRSVDEILRIIDAIQHH 163
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161  


Chain F from PDB  Type:PROTEIN  Length:169
                                                                                                                                                                                                         
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...........eeeee.....eeeee.hhhh...eeeeee.........hhhhhhhhhhhhhhhhh.eeeeeee..hhhhhhhhhh.hhhhh.......eeee...hhhhhhh..ee...ee.eeeeee.....eeeeeee......hhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4l0u F   2 PTYVGKEAPFFKAEAVFGDNSFGEVNLTQFIGKKYVLLYFYPLDFTFVCPSEIIALDKALDAFHERNVELLGCSVDSKYTHLAWKKTPLAKGGIGNIKHTLLSDITKSISKDYNVLFDDSVSLRAFVLIDMNGIVQHLLVNNLAIGRSVDEILRIIDAIQHHEKYGDVC 170
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161         


Chain G from PDB  Type:PROTEIN  Length:171
                                                                                                                                                                                                           
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...........eeeee.....eeeee.hhhh...eeeeee.........hhhhhhhhhhhhhhhhh.eeeeeee..hhhhhhhhhh.hhhhh.......eeee...hhhhhhh..ee...ee.eeeeee.....eeeeeee......hhhhhhhhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4l0u G   2 PTYVGKEAPFFKAEAVFGDNSFGEVNLTQFIGKKYVLLYFYPLDFTFVCPSEIIALDKALDAFHERNVELLGCSVDSKYTHLAWKKTPLAKGGIGNIKHTLLSDITKSISKDYNVLFDDSVSLRAFVLIDMNGIVQHLLVNNLAIGRSVDEILRIIDAIQHHEKYGDVCPA 172
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171 


Chain H from PDB  Type:PROTEIN  Length:167
                                                                                                                                                                                                       
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...........eeeee.....eeeee.hhhh...eeeeee.........hhhhhhhhhhhhhhhhh.eeeeeee..hhhhhhhhhh.hhhhh.......eeee...hhhhhhh..ee...ee.eeeeee.....eeeeeee......hhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4l0u H   2 PTYVGKEAPFFKAEAVFGDNSFGEVNLTQFIGKKYVLLYFYPLDFTFVCPSEIIALDKALDAFHERNVELLGCSVDSKYTHLAWKKTPLAKGGIGNIKHTLLSDITKSISKDYNVLFDDSVSLRAFVLIDMNGIVQHLLVNNLAIGRSVDEILRIIDAIQHHEKYGD 168
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       


Chain I from PDB  Type:PROTEIN  Length:177
                                                                                                                                                                                                                 
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ............eeeee.....eeeee.hhhh...eeeeee.........hhhhhhhhhhhhhhhhh.eeeeeee..hhhhhhhhhhhhhhhh.......eeee...hhhhhhh..ee...ee.eeeeee.....eeeeeee......hhhhhhhhhhhhhhhhhhh.......... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4l0u I   1 SPTYVGKEAPFFKAEAVFGDNSFGEVNLTQFIGKKYVLLYFYPLDFTFVCPSEIIALDKALDAFHERNVELLGCSVDSKYTHLAWKKTPLAKGGIGNIKHTLLSDITKSISKDYNVLFDDSVSLRAFVLIDMNGIVQHLLVNNLAIGRSVDEILRIIDAIQHHEKYGDVCPANWQKG 177
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       


Chain J from PDB  Type:PROTEIN  Length:179
                                                                                                                                                                                                                   
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...........eeeee.....eeeee.hhh....eeeeee.........hhhhhhhhhhhhhhhhh.eeeeeee..hhhhhhhhhhhhhhhh.......eeee...hhhhhhh..ee...ee.eeeeee.....eeeeeee......hhhhhhhhhhhhhhh................. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4l0u J   2 PTYVGKEAPFFKAEAVFGDNSFGEVNLTQFIGKKYVLLYFYPLDFTFVCPSEIIALDKALDAFHERNVELLGCSVDSKYTHLAWKKTPLAKGGIGNIKHTLLSDITKSISKDYNVLFDDSVSLRAFVLIDMNGIVQHLLVNNLAIGRSVDEILRIIDAIQHHEKYGDVCPANWQKGKVS 180
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171
   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 4L0U)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4L0U)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4L0U)

(-) Gene Ontology  (5, 5)

Asymmetric/Biological Unit(hide GO term definitions)

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  Cis Peptide Bonds
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 Related Entries

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        A5K421_PLAVS | A5K421: 2h66 2i81

(-) Related Entries Specified in the PDB File

2h66 THIS ENTRY 4L0U REFLECS AN ALTERNATIVE MODELING OF X-RAY DATA R2H66SF (DEPOSITED BY THE STRUCTURAL GENOMICS CONSORTIUM). R/RFREE AND GEOMETRY IMPROVED, ~20 RESIDUES ADDED.
4l0w