1XWB - JenaLib

Asymmetric Unit (Jmol Viewer)

Asym. Unit - sites (Jmol Viewer)

Biological Unit 1 (Jmol Viewer)

Biol. Unit 1 - sites (Jmol Viewer)

Biological Unit 2 (Jmol Viewer)

Biological Unit 3 (Jmol Viewer)

Biological Unit 4 (Jmol Viewer)

Biological Unit 5 (Jmol Viewer)

Title :   DROSPOHILA THIOREDOXIN, OXIDIZED, P42212

Authors :   M. C. Wahl, A. Irmler, B. Hecker, R. H. Schirmer, K. Becker

Date :   29 Oct 04 (Deposition) - 16 Nov 04 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.20

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)
Biol. Unit 5: A (1x),B (1x)

Keywords :   Dimerization, Drosophila Melanogaster, Redox Regulation, Thioredoxin, X-Ray Crystal Structure, Electron Transport (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   M. C. Wahl, A. Irmler, B. Hecker, R. H. Schirmer, K. Becker
Comparative Structural Analysis Of Oxidized And Reduced Thioredoxin From Drosophila Melanogaster
J. Mol. Biol. V. 345 1119 2005
PubMed-ID: 15644209 | Reference-DOI: 10.1016/J.JMB.2004.11.004

Molecule 1 - THIOREDOXIN
	Chains	:	A, B, C, D
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21(DE3)
	Expression System Plasmid	:	PQE-30
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Gene	:	TRX-2
	Organism Common	:	FRUIT FLY
	Organism Scientific	:	DROSOPHILA MELANOGASTER
	Organism Taxid	:	7227

		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
Biological Unit 5 (1x)	:	A (1x)	B (1x)

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 3)

No.	Name	Count	Type	Full Name
1	CD	3	Ligand/Ion	CADMIUM ION

Biological Unit 1 (0, 0)

No.	Name	Count	Type	Full Name
1	CD	-1	Ligand/Ion	CADMIUM ION

Biological Unit 2 (0, 0)

No.	Name	Count	Type	Full Name
1	CD	-1	Ligand/Ion	CADMIUM ION

Biological Unit 3 (0, 0)

No.	Name	Count	Type	Full Name
1	CD	-1	Ligand/Ion	CADMIUM ION

Biological Unit 4 (0, 0)

No.	Name	Count	Type	Full Name
1	CD	-1	Ligand/Ion	CADMIUM ION

Biological Unit 5 (0, 0)

No.	Name	Count	Type	Full Name
1	CD	-1	Ligand/Ion	CADMIUM ION

Asymmetric Unit (3, 3)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	THR A:30 , ASP A:61 , HOH A:830 , HOH A:854 , GLU B:64	BINDING SITE FOR RESIDUE CD A 801
2	AC2	SOFTWARE	GLU B:88 , HOH B:845 , GLU C:88 , HOH C:117 , HOH C:137 , HOH C:142	BINDING SITE FOR RESIDUE CD B 802
3	AC3	SOFTWARE	GLN D:48 , PHE D:49 , GLU D:99	BINDING SITE FOR RESIDUE CD D 803

Asymmetric Unit

No.	Residues
1	A:32	-	A:35
2	B:32	-	B:35
3	C:32	-	C:35
4	D:32	-	D:35

Asymmetric Unit

No.	Residues
1	Met A:75	-	Pro A:76
2	Met B:75	-	Pro B:76
3	Met C:75	-	Pro C:76
4	Met D:75	-	Pro D:76

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

Asymmetric Unit (2, 8)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	THIOREDOXIN_2	PS51352	Thioredoxin domain profile.	THIO2_DROME	4-114	4	A:7-106 B:7-106 C:7-106 D:7-106
2	THIOREDOXIN_1	PS00194	Thioredoxin family active site.	THIO2_DROME	32-50	4	A:24-42 B:24-42 C:24-42 D:24-42

Biological Unit 1 (2, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	THIOREDOXIN_2	PS51352	Thioredoxin domain profile.	THIO2_DROME	4-114	1	A:7-106 - - -
2	THIOREDOXIN_1	PS00194	Thioredoxin family active site.	THIO2_DROME	32-50	1	A:24-42 - - -

Biological Unit 2 (2, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	THIOREDOXIN_2	PS51352	Thioredoxin domain profile.	THIO2_DROME	4-114	1	- B:7-106 - -
2	THIOREDOXIN_1	PS00194	Thioredoxin family active site.	THIO2_DROME	32-50	1	- B:24-42 - -

Biological Unit 3 (2, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	THIOREDOXIN_2	PS51352	Thioredoxin domain profile.	THIO2_DROME	4-114	1	- - C:7-106 -
2	THIOREDOXIN_1	PS00194	Thioredoxin family active site.	THIO2_DROME	32-50	1	- - C:24-42 -

Biological Unit 4 (2, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	THIOREDOXIN_2	PS51352	Thioredoxin domain profile.	THIO2_DROME	4-114	1	- - - D:7-106
2	THIOREDOXIN_1	PS00194	Thioredoxin family active site.	THIO2_DROME	32-50	1	- - - D:24-42

Biological Unit 5 (2, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	THIOREDOXIN_2	PS51352	Thioredoxin domain profile.	THIO2_DROME	4-114	2	A:7-106 B:7-106 - -
2	THIOREDOXIN_1	PS00194	Thioredoxin family active site.	THIO2_DROME	32-50	2	A:24-42 B:24-42 - -

(no "Exon" information available for 1XWB)

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:106
 aligned with THIO2_DROME | Q9V429 from UniProtKB/Swiss-Prot  Length:114

    Alignment length:114
                                    10        20        30        40        50        60        70        80        90       100       110    
          THIO2_DROME     1 MMILLRDSTNLHFHLQADLDGQLTKASGKLVVLDFFATWCGPCKMISPKLVELSTQFADNVVVLKVDVDECEDIAMEYNISSMPTFVFLKNGVKVEEFAGANAKRLEDVIKANI 114
               SCOP domains d1xwba_         A: Thioredoxin                                                                                     SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eee..h--------hhhhhhhhhhhh..eeeeeee...hhhhhhhhhhhhhhhhhh...eeeeeee...hhhhhhhh......eeeeee..eeeeeee..hhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                PROSITE (1) ---THIOREDOXIN_2  PDB: A:7-106 UniProt: 4-114                                                                      PROSITE (1)
                PROSITE (2) -------------------------------THIOREDOXIN_1      ---------------------------------------------------------------- PROSITE (2)
                 Transcript ------------------------------------------------------------------------------------------------------------------ Transcript
                 1xwb A   1 MVYQVKD--------KADLDGQLTKASGKLVVLDFFATWCGPCKMISPKLVELSTQFADNVVVLKVDVDECEDIAMEYNISSMPTFVFLKNGVKVEEFAGANAKRLEDVIKANI 106
                                  |  -     |  12        22        32        42        52        62        72        82        92       102    
                                  7        8

Chain B from PDB  Type:PROTEIN  Length:106
 aligned with THIO2_DROME | Q9V429 from UniProtKB/Swiss-Prot  Length:114

    Alignment length:114
                                    10        20        30        40        50        60        70        80        90       100       110    
          THIO2_DROME     1 MMILLRDSTNLHFHLQADLDGQLTKASGKLVVLDFFATWCGPCKMISPKLVELSTQFADNVVVLKVDVDECEDIAMEYNISSMPTFVFLKNGVKVEEFAGANAKRLEDVIKANI 114
               SCOP domains d1xwbb_         B: Thioredoxin                                                                                     SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..ee..h--------hhhhhhhhhhhh..eeeeeee...hhhhhhhhhhhhhhhhhh...eeeeeee...hhhhhhhh......eeeeee..eeeeeee..hhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                PROSITE (1) ---THIOREDOXIN_2  PDB: B:7-106 UniProt: 4-114                                                                      PROSITE (1)
                PROSITE (2) -------------------------------THIOREDOXIN_1      ---------------------------------------------------------------- PROSITE (2)
                 Transcript ------------------------------------------------------------------------------------------------------------------ Transcript
                 1xwb B   1 MVYQVKD--------KADLDGQLTKASGKLVVLDFFATWCGPCKMISPKLVELSTQFADNVVVLKVDVDECEDIAMEYNISSMPTFVFLKNGVKVEEFAGANAKRLEDVIKANI 106
                                  |  -     |  12        22        32        42        52        62        72        82        92       102    
                                  7        8

Chain C from PDB  Type:PROTEIN  Length:106
 aligned with THIO2_DROME | Q9V429 from UniProtKB/Swiss-Prot  Length:114

    Alignment length:114
                                    10        20        30        40        50        60        70        80        90       100       110    
          THIO2_DROME     1 MMILLRDSTNLHFHLQADLDGQLTKASGKLVVLDFFATWCGPCKMISPKLVELSTQFADNVVVLKVDVDECEDIAMEYNISSMPTFVFLKNGVKVEEFAGANAKRLEDVIKANI 114
               SCOP domains d1xwbc_         C: Thioredoxin                                                                                     SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..ee..h--------hhhhhhhhhhhh..eeeeeee...hhhhhhhhhhhhhhhhhh...eeeeeee...hhhhhhhh......eeeeee..eeeeeee..hhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                PROSITE (1) ---THIOREDOXIN_2  PDB: C:7-106 UniProt: 4-114                                                                      PROSITE (1)
                PROSITE (2) -------------------------------THIOREDOXIN_1      ---------------------------------------------------------------- PROSITE (2)
                 Transcript ------------------------------------------------------------------------------------------------------------------ Transcript
                 1xwb C   1 MVYQVKD--------KADLDGQLTKASGKLVVLDFFATWCGPCKMISPKLVELSTQFADNVVVLKVDVDECEDIAMEYNISSMPTFVFLKNGVKVEEFAGANAKRLEDVIKANI 106
                                  |  -     |  12        22        32        42        52        62        72        82        92       102    
                                  7        8

Chain D from PDB  Type:PROTEIN  Length:106
 aligned with THIO2_DROME | Q9V429 from UniProtKB/Swiss-Prot  Length:114

    Alignment length:114
                                    10        20        30        40        50        60        70        80        90       100       110    
          THIO2_DROME     1 MMILLRDSTNLHFHLQADLDGQLTKASGKLVVLDFFATWCGPCKMISPKLVELSTQFADNVVVLKVDVDECEDIAMEYNISSMPTFVFLKNGVKVEEFAGANAKRLEDVIKANI 114
               SCOP domains d1xwbd_         D: Thioredoxin                                                                                     SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------ CATH domains
           Pfam domains (1) ----------------Thioredoxin-1xwbD01 D:9-105                                                                      - Pfam domains (1)
           Pfam domains (2) ----------------Thioredoxin-1xwbD02 D:9-105                                                                      - Pfam domains (2)
           Pfam domains (3) ----------------Thioredoxin-1xwbD03 D:9-105                                                                      - Pfam domains (3)
           Pfam domains (4) ----------------Thioredoxin-1xwbD04 D:9-105                                                                      - Pfam domains (4)
         Sec.struct. author ..ee..h--------hhhhhhhhhhh...eeeeeee...hhhhhhhhhhhhhhhhhh...eeeeeee...hhhhhhhh......eeeee....eeeeee..hhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                PROSITE (1) ---THIOREDOXIN_2  PDB: D:7-106 UniProt: 4-114                                                                      PROSITE (1)
                PROSITE (2) -------------------------------THIOREDOXIN_1      ---------------------------------------------------------------- PROSITE (2)
                 Transcript ------------------------------------------------------------------------------------------------------------------ Transcript
                 1xwb D   1 MVYQVKD--------KADLDGQLTKASGKLVVLDFFATWCGPCKMISPKLVELSTQFADNVVVLKVDVDECEDIAMEYNISSMPTFVFLKNGVKVEEFAGANAKRLEDVIKANI 106
                                  |  -     |  12        22        32        42        52        62        72        82        92       102    
                                  7        8

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: Thioltransferase (167)

Protein domain: Thioredoxin (106)

Fruit fly (Drosophila melanogaster) [TaxId: 7227] (4)

1a	d1xwba_	A:
1b	d1xwbb_	B:
1c	d1xwbc_	C:
1d	d1xwbd_	D:

(no "CATH Domain" information available for 1XWB)

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: Thioredoxin (367)

Family: Thioredoxin (82)

Drosophila melanogaster (Fruit fly) (3)

1a	Thioredoxin-1xwbD01	D:9-105
1b	Thioredoxin-1xwbD02	D:9-105
1c	Thioredoxin-1xwbD03	D:9-105
1d	Thioredoxin-1xwbD04	D:9-105

Asymmetric Unit(hide GO term definitions)

Chain A,B,C,D (THIO2_DROME | Q9V429)

molecular function
	GO:0015036	disulfide oxidoreductase activity	Catalysis of the reaction: substrate with reduced sulfide groups = substrate with oxidized disulfide bonds.
	GO:0016671	oxidoreductase activity, acting on a sulfur group of donors, disulfide as acceptor	Catalysis of an oxidation-reduction (redox) reaction in which a sulfur-containing group acts as a hydrogen or electron donor and reduces disulfide.
	GO:0015035	protein disulfide oxidoreductase activity	Catalysis of the reaction: a protein with reduced sulfide groups = a protein with oxidized disulfide bonds.
biological process
	GO:0045454	cell redox homeostasis	Any process that maintains the redox environment of a cell or compartment within a cell.
	GO:0006974	cellular response to DNA damage stimulus	Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus indicating damage to its DNA from environmental insults or errors during metabolism.
	GO:0034599	cellular response to oxidative stress	Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of oxidative stress, a state often resulting from exposure to high levels of reactive oxygen species, e.g. superoxide anions, hydrogen peroxide (H2O2), and hydroxyl radicals.
	GO:0050832	defense response to fungus	Reactions triggered in response to the presence of a fungus that act to protect the cell or organism.
	GO:0008340	determination of adult lifespan	The control of viability and duration in the adult phase of the life-cycle.
	GO:0006662	glycerol ether metabolic process	The chemical reactions and pathways involving glycerol ethers, any anhydride formed between two organic hydroxy compounds, one of which is glycerol.
	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.
	GO:0006457	protein folding	The process of assisting in the covalent and noncovalent assembly of single chain polypeptides or multisubunit complexes into the correct tertiary structure.
	GO:0006979	response to oxidative stress	Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of oxidative stress, a state often resulting from exposure to high levels of reactive oxygen species, e.g. superoxide anions, hydrogen peroxide (H2O2), and hydroxyl radicals.
	GO:0000103	sulfate assimilation	The pathways by which inorganic sulfate is processed and incorporated into sulfated compounds.
cellular component
	GO:0005739	mitochondrion	A semiautonomous, self replicating organelle that occurs in varying numbers, shapes, and sizes in the cytoplasm of virtually all eukaryotic cells. It is notably the site of tissue respiration.
	GO:0005634	nucleus	A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.

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	Cis Peptide Bonds
		Met A:75 - Pro A:76	[ RasMol ]
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		Met C:75 - Pro C:76	[ RasMol ]
		Met D:75 - Pro D:76	[ RasMol ]

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	1xwb
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	THIO2_DROME \| Q9V429
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UniProtKB/Swiss-Prot
	THIO2_DROME \| Q9V429	:	1xw9 1xwa 1xwc

1xw9	OXIDIZED DROSPOHILA THIOREDOXIN IN SPACE GROUP P21
1xwa	OXIDIZED DROSPOHILA THIOREDOXIN IN SPACE GROUP P41212
1xwc	REDUCED DROSPOHILA THIOREDOXIN IN SPACE GROUP P6522

Description

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Ligands, Modified Residues, Ions (1, 3)

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