2I81 - JenaLib

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Title :   CRYSTAL STRUCTURE OF PLASMODIUM VIVAX 2-CYS PEROXIREDOXIN, REDUCED

Authors :   J. D. Artz, W. Qiu, A. Dong, J. Lew, H. Ren, Y. Zhao, I. Kozieradski, A. M. Edwards, C. H. Arrowsmith, J. Weigelt, M. Sundstrom, A. Bochkarev, R. Hui, Structural Genomics Consortium (Sgc)

Date :   31 Aug 06 (Deposition) - 19 Sep 06 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.45

Chains :   Asym. Unit : A,B,C,D,E
Biol. Unit 1: A,B,C,D,E  (2x)

Keywords :   Peroxiredoxin, Structural Genomics Consortium, Sgc, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   J. D. Artz, W. Qiu, A. Dong, J. Lew, H. Ren, Y. Zhao, I. Kozieradski, A. M. Edwards, C. H. Arrowsmith, J. Weigelt, M. Sundstrom, A. Bochkarev, R. Hui
Crystal Structure Of Plasmodium Vivax 2-Cys Peroxiredoxin, Reduced
To Be Published
PubMed: search
(for further references see the PDB file header)

Molecule 1 - 2-CYS PEROXIREDOXIN
	Chains	:	A, B, C, D, E
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	P28A-THROMBIN-LIC
	Expression System Strain	:	BL21-(DE3)-ROSETTA OXFORD
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Organism Scientific	:	PLASMODIUM VIVAX SAI-1
	Organism Taxid	:	126793
	Strain	:	SALVADOR I

		1	2	3	4	5
Asymmetric Unit	:	A	B	C	D	E
Biological Unit 1 (2x)	:	A	B	C	D	E

Summary Information (see also Sequences/Alignments below)

(no "Ligand,Modified Residues,Ions" information available for 2I81)

(no "Site" information available for 2I81)

(no "SS Bond" information available for 2I81)

Asymmetric Unit

No.	Residues
1	Lys A:176	-	Gly A:177
2	Glu A:186	-	Gly A:187
3	Lys B:176	-	Gly B:177
4	Glu B:186	-	Gly B:187
5	Ser B:193	-	Thr B:194
6	Lys C:176	-	Gly C:177
7	Glu C:186	-	Gly C:187
8	Ser C:193	-	Thr C:194
9	Lys D:165	-	Tyr D:166
10	Leu E:144	-	Ala E:145
11	Gly E:147	-	Arg E:148
12	Ala E:159	-	Ile E:160

(no "SAP(SNP)/Variant" information available for 2I81)

(no "PROSITE Motif" information available for 2I81)

(no "Exon" information available for 2I81)

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:193
 aligned with A5K421_PLAVS | A5K421 from UniProtKB/TrEMBL  Length:195

    Alignment length:193
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191   
         A5K421_PLAVS     2 PTYVGKEAPFFKAEAVFGDNSFGEVNLTQFIGKKYVLLYFYPLDFTFVCPSEIIALDKALDAFHERNVELLGCSVDSKYTHLAWKKTPLAKGGIGNIKHTLLSDITKSISKDYNVLFDDSVSLRAFVLIDMNGIVQHLLVNNLAIGRSVDEILRIIDAIQHHEKYGDVCPANWQKGKVSMKPSEEGVAQYLST 194
               SCOP domains d2i81a_ A: automated matches                                                                                                                                                                      SCOP domains
               CATH domains 2i81A00 A:2-194 Glutaredoxin                                                                                                                                                                      CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...........eeeee.....eeeee.hhhh...eeeeee......hhhhhhhhhhhhhhhhhhhh.eeeeeee..hhhhhhhhhh.hhhhh.......eeee...hhhhhhh..ee...ee.eeeeee.....eeeeeee......hhhhhhhhhhhhhhhhhhh...................hhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2i81 A   2 PTYVGKEAPFFKAEAVFGDNSFGEVNLTQFIGKKYVLLYFYPLDFTFVCPSEIIALDKALDAFHERNVELLGCSVDSKYTHLAWKKTPLAKGGIGNIKHTLLSDITKSISKDYNVLFDDSVSLRAFVLIDMNGIVQHLLVNNLAIGRSVDEILRIIDAIQHHEKYGDVCPANWQKGKVSMKPSEEGVAQYLST 194
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191

Chain B from PDB  Type:PROTEIN  Length:193
 aligned with A5K421_PLAVS | A5K421 from UniProtKB/TrEMBL  Length:195

    Alignment length:193
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192   
         A5K421_PLAVS     3 TYVGKEAPFFKAEAVFGDNSFGEVNLTQFIGKKYVLLYFYPLDFTFVCPSEIIALDKALDAFHERNVELLGCSVDSKYTHLAWKKTPLAKGGIGNIKHTLLSDITKSISKDYNVLFDDSVSLRAFVLIDMNGIVQHLLVNNLAIGRSVDEILRIIDAIQHHEKYGDVCPANWQKGKVSMKPSEEGVAQYLSTL 195
               SCOP domains d2i81b_ B: automated matches                                                                                                                                                                      SCOP domains
               CATH domains 2i81B00 B:3-195 Glutaredoxin                                                                                                                                                                      CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..........eeeee.....eeeee.hhhh...eeeeee......hhhhhhhhhhhhhhhhhhhh.eeeeeee..hhhhhhhhhh.hhhhh.......eeee...hhhhhhh..ee...ee.eeeeee.....eeeeeee......hhhhhhhhhhhhhhhhhhh................hhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2i81 B   3 TYVGKEAPFFKAEAVFGDNSFGEVNLTQFIGKKYVLLYFYPLDFTFVCPSEIIALDKALDAFHERNVELLGCSVDSKYTHLAWKKTPLAKGGIGNIKHTLLSDITKSISKDYNVLFDDSVSLRAFVLIDMNGIVQHLLVNNLAIGRSVDEILRIIDAIQHHEKYGDVCPANWQKGKVSMKPSEEGVAQYLSTL 195
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192

Chain C from PDB  Type:PROTEIN  Length:193
 aligned with A5K421_PLAVS | A5K421 from UniProtKB/TrEMBL  Length:195

    Alignment length:193
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191   
         A5K421_PLAVS     2 PTYVGKEAPFFKAEAVFGDNSFGEVNLTQFIGKKYVLLYFYPLDFTFVCPSEIIALDKALDAFHERNVELLGCSVDSKYTHLAWKKTPLAKGGIGNIKHTLLSDITKSISKDYNVLFDDSVSLRAFVLIDMNGIVQHLLVNNLAIGRSVDEILRIIDAIQHHEKYGDVCPANWQKGKVSMKPSEEGVAQYLST 194
               SCOP domains d2i81c_ C: automated matches                                                                                                                                                                      SCOP domains
               CATH domains 2i81C00 C:2-194 Glutaredoxin                                                                                                                                                                      CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...........eeeee.....eeeee.hhhh...eeeeee......hhhhhhhhhhhhhhhhhhhh.eeeeeee..hhhhhhhhhh.hhhhh.......eeee...hhhhhhh..ee...ee.eeeeee.....eeeeeee......hhhhhhhhhhhhhhhhhhh...................hhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2i81 C   2 PTYVGKEAPFFKAEAVFGDNSFGEVNLTQFIGKKYVLLYFYPLDFTFVCPSEIIALDKALDAFHERNVELLGCSVDSKYTHLAWKKTPLAKGGIGNIKHTLLSDITKSISKDYNVLFDDSVSLRAFVLIDMNGIVQHLLVNNLAIGRSVDEILRIIDAIQHHEKYGDVCPANWQKGKVSMKPSEEGVAQYLST 194
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191

Chain D from PDB  Type:PROTEIN  Length:163
 aligned with A5K421_PLAVS | A5K421 from UniProtKB/TrEMBL  Length:195

    Alignment length:164
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162    
         A5K421_PLAVS     3 TYVGKEAPFFKAEAVFGDNSFGEVNLTQFIGKKYVLLYFYPLDFTFVCPSEIIALDKALDAFHERNVELLGCSVDSKYTHLAWKKTPLAKGGIGNIKHTLLSDITKSISKDYNVLFDDSVSLRAFVLIDMNGIVQHLLVNNLAIGRSVDEILRIIDAIQHHEKY 166
               SCOP domains d2i81d_ D: automated matches                                                                                                                                         SCOP domains
               CATH domains 2i81D00 D:3-166 Glutaredoxin                                                                                                                                         CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..........eeeee.....eeeee........eeeeee.......hhhhhhhhhhhhhhhhhhh.eeeeeee..hhhhhhhhhhhhhhhh.......eeee...hhhhhhh..ee...ee.eeeeee.....eeeeeee.-....hhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2i81 D   3 TYVGKEAPFFKAEAVFGDNSFGEVNLTQFIGKKYVLLYFYPLDFTFVCPSEIIALDKALDAFHERNVELLGCSVDSKYTHLAWKKTPLAKGGIGNIKHTLLSDITKSISKDYNVLFDDSVSLRAFVLIDMNGIVQHLLVNN-AIGRSVDEILRIIDAIQHHEKY 166
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142| |    152       162    
                                                                                                                                                                      143 |                     
                                                                                                                                                                        145

Chain E from PDB  Type:PROTEIN  Length:167
 aligned with A5K421_PLAVS | A5K421 from UniProtKB/TrEMBL  Length:195

    Alignment length:167
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       
         A5K421_PLAVS     2 PTYVGKEAPFFKAEAVFGDNSFGEVNLTQFIGKKYVLLYFYPLDFTFVCPSEIIALDKALDAFHERNVELLGCSVDSKYTHLAWKKTPLAKGGIGNIKHTLLSDITKSISKDYNVLFDDSVSLRAFVLIDMNGIVQHLLVNNLAIGRSVDEILRIIDAIQHHEKYGD 168
               SCOP domains d2i81e_ E: automated matches                                                                                                                                            SCOP domains
               CATH domains 2i81E00 E:2-168 Glutaredoxin                                                                                                                                            CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...........eeeee.....eeeee.hhhh...eeeeee.......hhhhhhhhhhhhhhhhhhh.eeeeeee..hhhhhhhhhhh............eeee...hhhhhhh..ee...ee.eeeeee.....eeeeeee......hhhhhhhhhh.......... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2i81 E   2 PTYVGKEAPFFKAEAVFGDNSFGEVNLTQFIGKKYVLLYFYPLDFTFVCPSEIIALDKALDAFHERNVELLGCSVDSKYTHLAWKKTPLAKGGIGNIKHTLLSDITKSISKDYNVLFDDSVSLRAFVLIDMNGIVQHLLVNNLAIGRSVDEILRIIDAIQHHEKYGD 168
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161

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 '\|'

Asymmetric Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: Alpha and beta proteins (a/b) (23833)

Fold: Thioredoxin fold (994)

Superfamily: Thioredoxin-like (992)

Family: automated matches (347)

Protein domain: automated matches (347)

Plasmodium vivax [TaxId: 126793] (1)

1a	d2i81a_	A:
1b	d2i81b_	B:
1c	d2i81c_	C:
1d	d2i81d_	D:
1e	d2i81e_	E:

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: 3-Layer(aba) Sandwich (12045)

Topology: Glutaredoxin (620)

Homologous Superfamily: Glutaredoxin (617)

Plasmodium vivax sai-1. Organism_taxid: 126793. Strain: salvador i. (1)

1a	2i81E00	E:2-168
1b	2i81D00	D:3-166
1c	2i81A00	A:2-194
1d	2i81C00	C:2-194
1e	2i81B00	B:3-195

(no "Pfam Domain" information available for 2I81)

Asymmetric Unit(hide GO term definitions)

Chain A,B,C,D,E (A5K421_PLAVS | A5K421)

molecular function
	GO:0016209	antioxidant activity	Inhibition of the reactions brought about by dioxygen (O2) or peroxides. Usually the antioxidant is effective because it can itself be more easily oxidized than the substance protected. The term is often applied to components that can trap free radicals, thereby breaking the chain reaction that normally leads to extensive biological damage.
	GO:0016491	oxidoreductase activity	Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced.
	GO:0051920	peroxiredoxin activity	Catalysis of the reaction: 2 R'-SH + ROOH = R'-S-S-R' + H2O + ROH.
biological process
	GO:0098869	cellular oxidant detoxification	Any process carried out at the cellular level that reduces or removes the toxicity superoxide radicals or hydrogen peroxide.
	GO:0055114	oxidation-reduction process	A metabolic process that results in the removal or addition of one or more electrons to or from a substance, with or without the concomitant removal or addition of a proton or protons.

Asymmetric Unit
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	Ligands, Modified Residues, Ions
(no "Ligands, Modified Residues, Ions" information available for 2i81)

	Sites
(no "Sites" information available for 2i81)

	Cis Peptide Bonds
		Ala E:159 - Ile E:160	[ RasMol ]
		Glu A:186 - Gly A:187	[ RasMol ]
		Glu B:186 - Gly B:187	[ RasMol ]
		Glu C:186 - Gly C:187	[ RasMol ]
		Gly E:147 - Arg E:148	[ RasMol ]
		Leu E:144 - Ala E:145	[ RasMol ]
		Lys A:176 - Gly A:177	[ RasMol ]
		Lys B:176 - Gly B:177	[ RasMol ]
		Lys C:176 - Gly C:177	[ RasMol ]
		Lys D:165 - Tyr D:166	[ RasMol ]
		Ser B:193 - Thr B:194	[ RasMol ]
		Ser C:193 - Thr C:194	[ RasMol ]

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	2i81
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	A5K421_PLAVS \| A5K421	:	2h66 4l0u

2h01	OXIDIZED 2-CYS PEROXIREDOXIN FROM PLASMODIUM YOELII
2h66	OXIDIZED 2-CYS PEROXIREDOXIN FROM PLASMODIUM VIVAX

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