3KIJ - 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)

Title :   CRYSTAL STRUCTURE OF THE HUMAN PDI-PEROXIDASE

Authors :   D. V. Nguyen, L. W. Ruddock

Date :   02 Nov 09 (Deposition) - 12 Jan 11 (Release) - 23 Feb 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.80

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

Keywords :   Human Pdi-Peroxidase, Glutathione Peroxidase, Membrane, Oxidoreductase, Peroxidase, Transmembrane (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   V. D. Nguyen, M. J. Saaranen, A. R. Karala, A. K. Lappi, L. Wang, I. B. Raykhel, H. I. Alanen, K. E. Salo, C. C. Wang, L. W. Ruddock
Two Endoplasmic Reticulum Pdi Peroxidases Increase The Efficiency Of The Use Of Peroxide During Disulfide Bond Formation.
J. Mol. Biol. V. 406 503 2011
PubMed-ID: 21215271 | Reference-DOI: 10.1016/J.JMB.2010.12.039

Molecule 1 - PROBABLE GLUTATHIONE PEROXIDASE 8
	Chains	:	A, B, C
	EC Number	:	1.11.1.9
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET23A
	Expression System Strain	:	BL21(DE3)PLYSSRARE
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Fragment	:	UNP RESIDUES 38-209
	Gene	:	GPX8, GPX8_HUMAN, UNQ847/PRO1785
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Strain	:	HOMO SAPIENS

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 1)

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

Biological Unit 1 (0, 0)

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

Asymmetric Unit (1, 1)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	GLN A:80 , ARG A:84 , HOH A:340 , GLN B:80 , ARG B:84 , HOH B:247 , HOH B:323 , HOH B:566 , GLN C:80 , ARG C:84	BINDING SITE FOR RESIDUE SO4 B 1

(no "SS Bond" information available for 3KIJ)

Asymmetric Unit

No.	Residues
1	Gly A:97	-	Pro A:98
2	Gly B:97	-	Pro B:98
3	Gly C:97	-	Pro C:98

Asymmetric Unit (1, 3)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_060456	K	182	R	GPX8_HUMAN	Polymorphism	381852	A/B/C	R	182	R

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

Biological Unit 1 (1, 1)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_060456	K	182	R	GPX8_HUMAN	Polymorphism	381852	A	R	182	R

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

Biological Unit 2 (1, 1)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_060456	K	182	R	GPX8_HUMAN	Polymorphism	381852	B	R	182	R

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

Biological Unit 3 (1, 1)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_060456	K	182	R	GPX8_HUMAN	Polymorphism	381852	C	R	182	R

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

Asymmetric Unit (1, 3)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	GLUTATHIONE_PEROXID_2	PS00763	Glutathione peroxidases signature 2.	GPX8_HUMAN	104-111	3	A:104-111 B:104-111 C:104-111

Biological Unit 1 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	GLUTATHIONE_PEROXID_2	PS00763	Glutathione peroxidases signature 2.	GPX8_HUMAN	104-111	1	A:104-111 - -

Biological Unit 2 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	GLUTATHIONE_PEROXID_2	PS00763	Glutathione peroxidases signature 2.	GPX8_HUMAN	104-111	1	- B:104-111 -

Biological Unit 3 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	GLUTATHIONE_PEROXID_2	PS00763	Glutathione peroxidases signature 2.	GPX8_HUMAN	104-111	1	- - C:104-111

(no "Exon" information available for 3KIJ)

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:171
 aligned with GPX8_HUMAN | Q8TED1 from UniProtKB/Swiss-Prot  Length:209

    Alignment length:171
                                    48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208 
           GPX8_HUMAN    39 FLKPKINSFYAFEVKDAKGRTVSLEKYKGKVSLVVNVASDCQLTDRNYLGLKELHKEFGPSHFSVLAFPCNQFGESEPRPSKEVESFARKNYGVTFPIFHKIKILGSEGEPAFRFLVDSSKKEPRWNFWKYLVNPEGQVVKFWKPEEPIEVIRPDIAALVRQVIIKKKEDL 209
               SCOP domains d3kija_ A: automated matches                                                                                                                                                SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......hhhh.eee.....eee.hhhh..eeeeeee.....hhhhhhhhhhhhhhhhh...eeeeeee..........hhhhhhhhhhhhhh................hhhhhhhhhhhh........eeee.....eeeee....hhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -----------------------------------------------------------------------------------------------------------------------------------------------R--------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------GLUTATHI-------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3kij A  39 FLKPKINSFYAFEVKDAKGRTVSLEKYKGKVSLVVNVASDCQLTDRNYLGLKELHKEFGPSHFSVLAFPCNQFGESEPRPSKEVESFARKNYGVTFPIFHKIKILGSEGEPAFRFLVDSSKKEPRWNFWKYLVNPEGQVVKFWRPEEPIEVIRPDIAALVRQVIIKKKEDL 209
                                    48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208

Chain B from PDB  Type:PROTEIN  Length:171
 aligned with GPX8_HUMAN | Q8TED1 from UniProtKB/Swiss-Prot  Length:209

    Alignment length:171
                                    48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208 
           GPX8_HUMAN    39 FLKPKINSFYAFEVKDAKGRTVSLEKYKGKVSLVVNVASDCQLTDRNYLGLKELHKEFGPSHFSVLAFPCNQFGESEPRPSKEVESFARKNYGVTFPIFHKIKILGSEGEPAFRFLVDSSKKEPRWNFWKYLVNPEGQVVKFWKPEEPIEVIRPDIAALVRQVIIKKKEDL 209
               SCOP domains d3kijb_ B: automated matches                                                                                                                                                SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhh.eee.....eee.hhhh..eeeeeee.....hhhhhhhhhhhhhhhhh...eeeeeee..........hhhhhhhhhhhhhh................hhhhhhhhhhhh........eeee.....eeeee....hhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -----------------------------------------------------------------------------------------------------------------------------------------------R--------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------GLUTATHI-------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3kij B  39 FLKPKINSFYAFEVKDAKGRTVSLEKYKGKVSLVVNVASDCQLTDRNYLGLKELHKEFGPSHFSVLAFPCNQFGESEPRPSKEVESFARKNYGVTFPIFHKIKILGSEGEPAFRFLVDSSKKEPRWNFWKYLVNPEGQVVKFWRPEEPIEVIRPDIAALVRQVIIKKKEDL 209
                                    48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208

Chain C from PDB  Type:PROTEIN  Length:168
 aligned with GPX8_HUMAN | Q8TED1 from UniProtKB/Swiss-Prot  Length:209

    Alignment length:168
                                    48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198        
           GPX8_HUMAN    39 FLKPKINSFYAFEVKDAKGRTVSLEKYKGKVSLVVNVASDCQLTDRNYLGLKELHKEFGPSHFSVLAFPCNQFGESEPRPSKEVESFARKNYGVTFPIFHKIKILGSEGEPAFRFLVDSSKKEPRWNFWKYLVNPEGQVVKFWKPEEPIEVIRPDIAALVRQVIIKKK 206
               SCOP domains d3kijc_ C: automated matches                                                                                                                                             SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
           Pfam domains (1) --------GSHPx-3kijC01 C:47-155                                                                                       --------------------------------------------------- Pfam domains (1)
           Pfam domains (2) --------GSHPx-3kijC02 C:47-155                                                                                       --------------------------------------------------- Pfam domains (2)
           Pfam domains (3) --------GSHPx-3kijC03 C:47-155                                                                                       --------------------------------------------------- Pfam domains (3)
         Sec.struct. author .......hhhh.eee.....eee.hhhh..eeeeeee.....hhhhhhhhhhhhhhhhh...eeeeeee..........hhhhhhhhhhhhhh................hhhhhhhhhhhh........eeee.....eeeee....hhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -----------------------------------------------------------------------------------------------------------------------------------------------R------------------------ SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------GLUTATHI----------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3kij C  39 FLKPKINSFYAFEVKDAKGRTVSLEKYKGKVSLVVNVASDCQLTDRNYLGLKELHKEFGPSHFSVLAFPCNQFGESEPRPSKEVESFARKNYGVTFPIFHKIKILGSEGEPAFRFLVDSSKKEPRWNFWKYLVNPEGQVVKFWRPEEPIEVIRPDIAALVRQVIIKKK 206
                                    48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198

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)

Human (Homo sapiens) [TaxId: 9606] (87)

1a	d3kija_	A:
1b	d3kijb_	B:
1c	d3kijc_	C:

(no "CATH Domain" information available for 3KIJ)

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: Thioredoxin (367)

Family: GSHPx (11)

Homo sapiens (Human) (4)

1a	GSHPx-3kijC01	C:47-155
1b	GSHPx-3kijC02	C:47-155
1c	GSHPx-3kijC03	C:47-155

Asymmetric Unit(hide GO term definitions)

Chain A,B,C (GPX8_HUMAN | Q8TED1)

molecular function
	GO:0004602	glutathione peroxidase activity	Catalysis of the reaction: 2 glutathione + hydrogen peroxide = oxidized glutathione + 2 H2O.
	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:0004601	peroxidase activity	Catalysis of the reaction: donor + hydrogen peroxide = oxidized donor + 2 H2O.
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.
	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:0000302	response to reactive oxygen species	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 a reactive oxygen species stimulus. Reactive oxygen species include singlet oxygen, superoxide, and oxygen free radicals.
cellular component
	GO:0005788	endoplasmic reticulum lumen	The volume enclosed by the membranes of the endoplasmic reticulum.
	GO:0016021	integral component of membrane	The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
	GO:0016020	membrane	A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.

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	Sites
		AC1	[ RasMol ]	+environment [ RasMol ]

	Cis Peptide Bonds
		Gly A:97 - Pro A:98	[ RasMol ]
		Gly B:97 - Pro B:98	[ RasMol ]
		Gly C:97 - Pro C:98	[ RasMol ]

Biological Units
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	3kij
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(no "Related Entries Specified in the PDB File" available for 3KIJ)

Description

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Chains, Units

Ligands, Modified Residues, Ions (1, 1)

Sites (1, 1)

SS Bonds (0, 0)

Cis Peptide Bonds (3, 3)

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