1TP9 - JenaLib

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Asymmetric Unit (Jmol Viewer)

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Biol. Unit 1 - sites (Jmol Viewer)

Biological Unit 2 (Jmol Viewer)

Biological Unit 3 (Jmol Viewer)

Biological Unit 4 (Jmol Viewer)

Title :   PRX D (TYPE II) FROM POPULUS TREMULA

Authors :   A. Echalier, X. Trivelli, C. Corbier, N. Rouhier, O. Walker, P. Tsan, J. P. Jacquot, I. Krimm, J. M. Lancelin

Date :   16 Jun 04 (Deposition) - 26 Apr 05 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.62

Chains :   Asym. Unit : A,B,C,D
Biol. Unit 1: A  (1x)
Biol. Unit 2: B  (1x)
Biol. Unit 3: C  (1x)
Biol. Unit 4: D  (1x)

Keywords :   Peroxiredoxin, Oligomer, Thioredoxin Fold, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   A. Echalier, X. Trivelli, C. Corbier, N. Rouhier, O. Walker, P. Tsan, J. P. Jacquot, A. Aubry, I. Krimm, J. M. Lancelin
Crystal Structure And Solution Nmr Dynamics Of A D (Type Ii) Peroxiredoxin Glutaredoxin And Thioredoxin Dependent: A New Insight Into The Peroxiredoxin Oligomerism
Biochemistry V. 44 1755 2005
PubMed-ID: 15697201 | Reference-DOI: 10.1021/BI048226S
(for further references see the PDB file header)

Molecule 1 - PEROXIREDOXIN
	Chains	:	A, B, C, D
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21
	Expression System Plasmid	:	PET3D
	Expression System Strain	:	BL21
	Expression System Taxid	:	511693
	Expression System Vector Type	:	PLASMID
	Organism Scientific	:	POPULUS TRICHOCARPA
	Organism Taxid	:	3694
	Synonym	:	PRX D (TYPE II)

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 2)

No.	Name	Count	Type	Full Name
1	SO4	2	Ligand/Ion	SULFATE ION

Biological Unit 1 (1, 1)

No.	Name	Count	Type	Full Name
1	SO4	1	Ligand/Ion	SULFATE ION

Biological Unit 2 (1, 1)

No.	Name	Count	Type	Full Name
1	SO4	1	Ligand/Ion	SULFATE ION

Biological Unit 3 (0, 0)

No.	Name	Count	Type	Full Name
1	SO4	-1	Ligand/Ion	SULFATE ION

Biological Unit 4 (0, 0)

No.	Name	Count	Type	Full Name
1	SO4	-1	Ligand/Ion	SULFATE ION

Asymmetric Unit (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	PRO A:49 , THR A:50 , LYS A:121 , HOH A:1317 , HOH A:1371 , HOH A:1439	BINDING SITE FOR RESIDUE SO4 A 1248
2	AC2	SOFTWARE	PRO B:49 , THR B:50 , HOH B:1366	BINDING SITE FOR RESIDUE SO4 B 1249

(no "SS Bond" information available for 1TP9)

(no "Cis Peptide Bond" information available for 1TP9)

(no "SAP(SNP)/Variant" information available for 1TP9)

(no "PROSITE Motif" information available for 1TP9)

(no "Exon" information available for 1TP9)

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:162
 aligned with A9PCL4_POPTR | A9PCL4 from UniProtKB/TrEMBL  Length:162

    Alignment length:162
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160  
         A9PCL4_POPTR     1 MAPIAVGDVLPDGKLAYFDEQDQLQEVSVHSLVAGKKVILFGVPGAFTPTCSLKHVPGFIEKAGELKSKGVTEILCISVNDPFVMKAWAKSYPENKHVKFLADGSATYTHALGLELNLQEKGLGTRSRRFALLVDDLKVKAANIEGGGEFTVSSADDILKDL 162
               SCOP domains d1tp9a1 A:1-162 Plant peroxiredoxin                                                                                                                                SCOP domains
               CATH domains 1tp9A00 A:1-162 Glutaredoxin                                                                                                                                       CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .............eeeee.....eeeeehhhhhh..eeeeeee....hhhhhhhhhhhhhhhhhhhhhh....eeeee..hhhhhhhhhhh......eeeee...hhhhhhh..eeee.....eeee..eeeeee..eeeeeee.........hhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1tp9 A   1 MAPIAVGDVLPDGKLAYFDEQDQLQEVSVHSLVAGKKVILFGVPGAFTPTCSLKHVPGFIEKAGELKSKGVTEILCISVNDPFVMKAWAKSYPENKHVKFLADGSATYTHALGLELDLQEKGLGTRSRRFALLVDDLKVKAANIEGGGEFTVSSAEDILKDL 162
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160

Chain A from PDB  Type:PROTEIN  Length:162
 aligned with Q8S3L0_9ROSI | Q8S3L0 from UniProtKB/TrEMBL  Length:162

    Alignment length:162
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160  
         Q8S3L0_9ROSI     1 MAPIAVGDVLPDGKLAYFDEQDQLQEVSVHSLVAGKKVILFGVPGAFTPTCSLKHVPGFIEKAGELKSKGVTEILCISVNDPFVMKAWAKSYPENKHVKFLADGSATYTHALGLELDLQEKGLGTRSRRFALLVDDLKVKAANIEGGGEFTVSSAEDILKDL 162
               SCOP domains d1tp9a1 A:1-162 Plant peroxiredoxin                                                                                                                                SCOP domains
               CATH domains 1tp9A00 A:1-162 Glutaredoxin                                                                                                                                       CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .............eeeee.....eeeeehhhhhh..eeeeeee....hhhhhhhhhhhhhhhhhhhhhh....eeeee..hhhhhhhhhhh......eeeee...hhhhhhh..eeee.....eeee..eeeeee..eeeeeee.........hhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1tp9 A   1 MAPIAVGDVLPDGKLAYFDEQDQLQEVSVHSLVAGKKVILFGVPGAFTPTCSLKHVPGFIEKAGELKSKGVTEILCISVNDPFVMKAWAKSYPENKHVKFLADGSATYTHALGLELDLQEKGLGTRSRRFALLVDDLKVKAANIEGGGEFTVSSAEDILKDL 162
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160

Chain B from PDB  Type:PROTEIN  Length:162
 aligned with A9PCL4_POPTR | A9PCL4 from UniProtKB/TrEMBL  Length:162

    Alignment length:162
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160  
         A9PCL4_POPTR     1 MAPIAVGDVLPDGKLAYFDEQDQLQEVSVHSLVAGKKVILFGVPGAFTPTCSLKHVPGFIEKAGELKSKGVTEILCISVNDPFVMKAWAKSYPENKHVKFLADGSATYTHALGLELNLQEKGLGTRSRRFALLVDDLKVKAANIEGGGEFTVSSADDILKDL 162
               SCOP domains d1tp9b_ B: automated matches                                                                                                                                       SCOP domains
               CATH domains 1tp9B00 B:1-162 Glutaredoxin                                                                                                                                       CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .............eeeee.....eeeeehhhhhh..eeeeee.....hhhhhhhhhhhhhhhhhhhhhh...eeeeee..hhhhhhhhhhh......eeeee...hhhhhhh..eeee.....eeee..eeeeee..eeeeeee.........hhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1tp9 B   1 MAPIAVGDVLPDGKLAYFDEQDQLQEVSVHSLVAGKKVILFGVPGAFTPTCSLKHVPGFIEKAGELKSKGVTEILCISVNDPFVMKAWAKSYPENKHVKFLADGSATYTHALGLELDLQEKGLGTRSRRFALLVDDLKVKAANIEGGGEFTVSSAEDILKDL 162
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160

Chain B from PDB  Type:PROTEIN  Length:162
 aligned with Q8S3L0_9ROSI | Q8S3L0 from UniProtKB/TrEMBL  Length:162

    Alignment length:162
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160  
         Q8S3L0_9ROSI     1 MAPIAVGDVLPDGKLAYFDEQDQLQEVSVHSLVAGKKVILFGVPGAFTPTCSLKHVPGFIEKAGELKSKGVTEILCISVNDPFVMKAWAKSYPENKHVKFLADGSATYTHALGLELDLQEKGLGTRSRRFALLVDDLKVKAANIEGGGEFTVSSAEDILKDL 162
               SCOP domains d1tp9b_ B: automated matches                                                                                                                                       SCOP domains
               CATH domains 1tp9B00 B:1-162 Glutaredoxin                                                                                                                                       CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .............eeeee.....eeeeehhhhhh..eeeeee.....hhhhhhhhhhhhhhhhhhhhhh...eeeeee..hhhhhhhhhhh......eeeee...hhhhhhh..eeee.....eeee..eeeeee..eeeeeee.........hhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1tp9 B   1 MAPIAVGDVLPDGKLAYFDEQDQLQEVSVHSLVAGKKVILFGVPGAFTPTCSLKHVPGFIEKAGELKSKGVTEILCISVNDPFVMKAWAKSYPENKHVKFLADGSATYTHALGLELDLQEKGLGTRSRRFALLVDDLKVKAANIEGGGEFTVSSAEDILKDL 162
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160

Chain C from PDB  Type:PROTEIN  Length:162
 aligned with A9PCL4_POPTR | A9PCL4 from UniProtKB/TrEMBL  Length:162

    Alignment length:162
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160  
         A9PCL4_POPTR     1 MAPIAVGDVLPDGKLAYFDEQDQLQEVSVHSLVAGKKVILFGVPGAFTPTCSLKHVPGFIEKAGELKSKGVTEILCISVNDPFVMKAWAKSYPENKHVKFLADGSATYTHALGLELNLQEKGLGTRSRRFALLVDDLKVKAANIEGGGEFTVSSADDILKDL 162
               SCOP domains d1tp9c_ C: automated matches                                                                                                                                       SCOP domains
               CATH domains 1tp9C00 C:1-162 Glutaredoxin                                                                                                                                       CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .............eeeee.....eeeeehhhhhh..eeeeee.....hhhhhhhhhhhhhhhhhhhhhh...eeeeee..hhhhhhhhhh.......eeeee...hhhhhhh..eee.......eee..eeeeee..eeeeeee.........hhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1tp9 C   1 MAPIAVGDVLPDGKLAYFDEQDQLQEVSVHSLVAGKKVILFGVPGAFTPTCSLKHVPGFIEKAGELKSKGVTEILCISVNDPFVMKAWAKSYPENKHVKFLADGSATYTHALGLELDLQEKGLGTRSRRFALLVDDLKVKAANIEGGGEFTVSSAEDILKDL 162
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160

Chain C from PDB  Type:PROTEIN  Length:162
 aligned with Q8S3L0_9ROSI | Q8S3L0 from UniProtKB/TrEMBL  Length:162

    Alignment length:162
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160  
         Q8S3L0_9ROSI     1 MAPIAVGDVLPDGKLAYFDEQDQLQEVSVHSLVAGKKVILFGVPGAFTPTCSLKHVPGFIEKAGELKSKGVTEILCISVNDPFVMKAWAKSYPENKHVKFLADGSATYTHALGLELDLQEKGLGTRSRRFALLVDDLKVKAANIEGGGEFTVSSAEDILKDL 162
               SCOP domains d1tp9c_ C: automated matches                                                                                                                                       SCOP domains
               CATH domains 1tp9C00 C:1-162 Glutaredoxin                                                                                                                                       CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .............eeeee.....eeeeehhhhhh..eeeeee.....hhhhhhhhhhhhhhhhhhhhhh...eeeeee..hhhhhhhhhh.......eeeee...hhhhhhh..eee.......eee..eeeeee..eeeeeee.........hhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1tp9 C   1 MAPIAVGDVLPDGKLAYFDEQDQLQEVSVHSLVAGKKVILFGVPGAFTPTCSLKHVPGFIEKAGELKSKGVTEILCISVNDPFVMKAWAKSYPENKHVKFLADGSATYTHALGLELDLQEKGLGTRSRRFALLVDDLKVKAANIEGGGEFTVSSAEDILKDL 162
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160

Chain D from PDB  Type:PROTEIN  Length:160
 aligned with A9PCL4_POPTR | A9PCL4 from UniProtKB/TrEMBL  Length:162

    Alignment length:160
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161
         A9PCL4_POPTR     2 APIAVGDVLPDGKLAYFDEQDQLQEVSVHSLVAGKKVILFGVPGAFTPTCSLKHVPGFIEKAGELKSKGVTEILCISVNDPFVMKAWAKSYPENKHVKFLADGSATYTHALGLELNLQEKGLGTRSRRFALLVDDLKVKAANIEGGGEFTVSSADDILKD 161
               SCOP domains d1tp9d_ D: automated matches                                                                                                                                     SCOP domains
               CATH domains 1tp9D00 D:2-161 Glutaredoxin                                                                                                                                     CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ............eeeee.....eeeeehhhhhh..eeeeeee....hhhhhhhhhhhhhhhhhhhhhh...eeeeee..hhhhhhhhhhh......eeeee...hhhhhhh..eee.hhhh..eee..eeeeee..eeeeeee.........hhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1tp9 D   2 APIAVGDVLPDGKLAYFDEQDQLQEVSVHSLVAGKKVILFGVPGAFTPTCSLKHVPGFIEKAGELKSKGVTEILCISVNDPFVMKAWAKSYPENKHVKFLADGSATYTHALGLELDLQEKGLGTRSRRFALLVDDLKVKAANIEGGGEFTVSSAEDILKD 161
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161

Chain D from PDB  Type:PROTEIN  Length:160
 aligned with Q8S3L0_9ROSI | Q8S3L0 from UniProtKB/TrEMBL  Length:162

    Alignment length:160
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161
         Q8S3L0_9ROSI     2 APIAVGDVLPDGKLAYFDEQDQLQEVSVHSLVAGKKVILFGVPGAFTPTCSLKHVPGFIEKAGELKSKGVTEILCISVNDPFVMKAWAKSYPENKHVKFLADGSATYTHALGLELDLQEKGLGTRSRRFALLVDDLKVKAANIEGGGEFTVSSAEDILKD 161
               SCOP domains d1tp9d_ D: automated matches                                                                                                                                     SCOP domains
               CATH domains 1tp9D00 D:2-161 Glutaredoxin                                                                                                                                     CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ............eeeee.....eeeeehhhhhh..eeeeeee....hhhhhhhhhhhhhhhhhhhhhh...eeeeee..hhhhhhhhhhh......eeeee...hhhhhhh..eee.hhhh..eee..eeeeee..eeeeeee.........hhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1tp9 D   2 APIAVGDVLPDGKLAYFDEQDQLQEVSVHSLVAGKKVILFGVPGAFTPTCSLKHVPGFIEKAGELKSKGVTEILCISVNDPFVMKAWAKSYPENKHVKFLADGSATYTHALGLELDLQEKGLGTRSRRFALLVDDLKVKAANIEGGGEFTVSSAEDILKD 161
                                    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)

Western balsam poplar (Populus trichocarpa) [TaxId: 3694] (2)

1a	d1tp9b_	B:
1b	d1tp9c_	C:
1c	d1tp9d_	D:

Family: Glutathione peroxidase-like (136)

Protein domain: Plant peroxiredoxin (1)

Western balsam poplar (Populus trichocarpa) [TaxId: 3694] (1)

d1tp9a1

A:1-162

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)

Populus trichocarpa. Organism_taxid: 3694. (1)

1a	1tp9D00	D:2-161
1b	1tp9A00	A:1-162
1c	1tp9B00	B:1-162
1d	1tp9C00	C:1-162

(no "Pfam Domain" information available for 1TP9)

Asymmetric Unit(hide GO term definitions)

Chain A,B,C,D (A9PCL4_POPTR | A9PCL4)

molecular function
	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.
biological process
	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.

Chain A,B,C,D (Q8S3L0_9ROSI | Q8S3L0)

molecular function
	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.
biological process
	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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	Cis Peptide Bonds
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	1tp9
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	A9PCL4_POPTR \| A9PCL4
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Description

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Ligands, Modified Residues, Ions (1, 2)

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