3CYN - 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)

Title :   THE STRUCTURE OF HUMAN GPX8

Authors :   K. L. Kavanagh, C. Johansson, W. W. Yue, G. Kochan, A. C. W. Pike, J. Murra A. K. Roos, P. Filippakopoulos, F. Von Delft, C. H. Arrowsmith, M. Wik A. M. Edwards, C. Bountra, U. Oppermann, Structural Genomics Conso (Sgc)

Date :   25 Apr 08 (Deposition) - 12 Aug 08 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.00

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

Keywords :   Thioredoxin Fold, Glutathione Peroxidase, Membrane, Oxidoreductase, Transmembrane, Structural Genomics, Structural Genomics Consortium, Sgc (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   K. L. Kavanagh, C. Johansson, W. W. Yue, G. Kochan, U. Oppermann
The Structure Of Human Gpx8
To Be Published
PubMed: search

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	:	PNIC-BSA4
	Expression System Strain	:	BL21 (DE3)
	Expression System Vector Type	:	PLASMID
	Fragment	:	RESIDUES 44-209
	Gene	:	LOC493869
	Organism Common	:	HUMAN
	Organism Scientific	:	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
Biological Unit 4 (1x)	:	A	B	C

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 9)

No.	Name	Count	Type	Full Name
1	GOL	3	Ligand/Ion	GLYCEROL
2	SO4	6	Ligand/Ion	SULFATE ION

Biological Unit 1 (2, 2)

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

Biological Unit 2 (2, 5)

No.	Name	Count	Type	Full Name
1	GOL	1	Ligand/Ion	GLYCEROL
2	SO4	4	Ligand/Ion	SULFATE ION

Biological Unit 3 (2, 2)

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

Biological Unit 4 (2, 9)

No.	Name	Count	Type	Full Name
1	GOL	3	Ligand/Ion	GLYCEROL
2	SO4	6	Ligand/Ion	SULFATE ION

Asymmetric Unit (9, 9)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	GLN A:80 , ARG A:84 , GLN B:80 , ARG B:84 , GLN C:80 , ARG C:84	BINDING SITE FOR RESIDUE SO4 B 1
2	AC2	SOFTWARE	LYS C:160 , ARG C:182	BINDING SITE FOR RESIDUE SO4 C 2
3	AC3	SOFTWARE	TRP A:164	BINDING SITE FOR RESIDUE SO4 B 3
4	AC4	SOFTWARE	LYS B:160 , PHE B:180 , ARG B:182 , GLY C:34 , THR C:35	BINDING SITE FOR RESIDUE SO4 B 4
5	AC5	SOFTWARE	ARG A:199 , GLN A:200 , ASN B:172 , LEU B:197 , GLN B:200	BINDING SITE FOR RESIDUE SO4 B 5
6	AC6	SOFTWARE	LYS A:160 , ARG A:182	BINDING SITE FOR RESIDUE SO4 A 6
7	AC7	SOFTWARE	SER A:119 , HIS A:138 , LYS A:139	BINDING SITE FOR RESIDUE GOL A 7
8	AC8	SOFTWARE	SER B:119 , HIS B:138 , LYS B:139	BINDING SITE FOR RESIDUE GOL B 8
9	AC9	SOFTWARE	SER C:119 , HIS C:138 , LYS C:139	BINDING SITE FOR RESIDUE GOL C 9

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

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)

Biological Unit 4 (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)

Asymmetric Unit (2, 6)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	GLUTATHIONE_PEROXID_3	PS51355	Glutathione peroxidase profile.	GPX8_HUMAN	37-204	3	A:44-204 B:38-204 C:44-204
2	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 (2, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	GLUTATHIONE_PEROXID_3	PS51355	Glutathione peroxidase profile.	GPX8_HUMAN	37-204	1	A:44-204 - -
2	GLUTATHIONE_PEROXID_2	PS00763	Glutathione peroxidases signature 2.	GPX8_HUMAN	104-111	1	A:104-111 - -

Biological Unit 2 (2, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	GLUTATHIONE_PEROXID_3	PS51355	Glutathione peroxidase profile.	GPX8_HUMAN	37-204	1	- B:38-204 -
2	GLUTATHIONE_PEROXID_2	PS00763	Glutathione peroxidases signature 2.	GPX8_HUMAN	104-111	1	- B:104-111 -

Biological Unit 3 (2, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	GLUTATHIONE_PEROXID_3	PS51355	Glutathione peroxidase profile.	GPX8_HUMAN	37-204	1	- - C:44-204
2	GLUTATHIONE_PEROXID_2	PS00763	Glutathione peroxidases signature 2.	GPX8_HUMAN	104-111	1	- - C:104-111

Biological Unit 4 (2, 6)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	GLUTATHIONE_PEROXID_3	PS51355	Glutathione peroxidase profile.	GPX8_HUMAN	37-204	3	A:44-204 B:38-204 C:44-204
2	GLUTATHIONE_PEROXID_2	PS00763	Glutathione peroxidases signature 2.	GPX8_HUMAN	104-111	3	A:104-111 B:104-111 C:104-111

(no "Exon" information available for 3CYN)

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:174
 aligned with GPX8_HUMAN | Q8TED1 from UniProtKB/Swiss-Prot  Length:209

    Alignment length:174
                                    45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205    
           GPX8_HUMAN    36 QLKFLKPKINSFYAFEVKDAKGRTVSLEKYKGKVSLVVNVASDCQLTDRNYLGLKELHKEFGPSHFSVLAFPCNQFGESEPRPSKEVESFARKNYGVTFPIFHKIKILGSEGEPAFRFLVDSSKKEPRWNFWKYLVNPEGQVVKFWKPEEPIEVIRPDIAALVRQVIIKKKEDL 209
               SCOP domains d3cyna_ A: automated matches                                                                                                                                                   SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .hhhhh....hhhh.eee.....eee.hhhh..eeeeeee.....hhhhhhhhhhhhhhhhh...eeeeeee..........hhhhhhhhhhhhhh................hhhhhhhhhhhh........eeee.....eeeee....hhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------R--------------------------- SAPs(SNPs)
                PROSITE (1) -GLUTATHIONE_PEROXID_3  PDB: A:44-204 UniProt: 37-204                                                                                                                    ----- PROSITE (1)
                PROSITE (2) --------------------------------------------------------------------GLUTATHI-------------------------------------------------------------------------------------------------- PROSITE (2)
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3cyn A  36 ENLYFQSMINSFYAFEVKDAKGRTVSLEKYKGKVSLVVNVASDCQLTDRNYLGLKELHKEFGPSHFSVLAFPCNQFGESEPRPSKEVESFARKNYGVTFPIFHKIKILGSEGEPAFRFLVDSSKKEPRWNFWKYLVNPEGQVVKFWRPEEPIEVIRPDIAALVRQVIIKKKEDL 209
                                    45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205

Chain B from PDB  Type:PROTEIN  Length:173
 aligned with GPX8_HUMAN | Q8TED1 from UniProtKB/Swiss-Prot  Length:209

    Alignment length:174
                                    45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205    
           GPX8_HUMAN    36 QLKFLKPKINSFYAFEVKDAKGRTVSLEKYKGKVSLVVNVASDCQLTDRNYLGLKELHKEFGPSHFSVLAFPCNQFGESEPRPSKEVESFARKNYGVTFPIFHKIKILGSEGEPAFRFLVDSSKKEPRWNFWKYLVNPEGQVVKFWKPEEPIEVIRPDIAALVRQVIIKKKEDL 209
               SCOP domains d3cynb _ B: automated matches                                                                                                                                                  SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author hhhhh.-...hhhh.eee.....eee.hhhh..eeeeeee.....hhhhhhhhhhhhhhhhh...eeeeeee..........hhhhhhhhhhhhhh................hhhhhhhhhhhh........eeee.....eeeee....hhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------R--------------------------- SAPs(SNPs)
                PROSITE (1) -GLUTATHIONE_PEROXID_3  PDB: B:38-204 UniProt: 37-204                                                                                                                    ----- PROSITE (1)
                PROSITE (2) --------------------------------------------------------------------GLUTATHI-------------------------------------------------------------------------------------------------- PROSITE (2)
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3cyn B  37 NLYFQS-MINSFYAFEVKDAKGRTVSLEKYKGKVSLVVNVASDCQLTDRNYLGLKELHKEFGPSHFSVLAFPCNQFGESEPRPSKEVESFARKNYGVTFPIFHKIKILGSEGEPAFRFLVDSSKKEPRWNFWKYLVNPEGQVVKFWRPEEPIEVIRPDIAALVRQVIIKKKEDL 209
                                 | |45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205    
                                42 |                                                                                                                                                                      
                                  43

Chain C from PDB  Type:PROTEIN  Length:176
 aligned with GPX8_HUMAN | Q8TED1 from UniProtKB/Swiss-Prot  Length:209

    Alignment length:197
                                    22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       
           GPX8_HUMAN    13 GPRAKVFAVLLSIVLCTVTLFLLQLKFLKPKINSFYAFEVKDAKGRTVSLEKYKGKVSLVVNVASDCQLTDRNYLGLKELHKEFGPSHFSVLAFPCNQFGESEPRPSKEVESFARKNYGVTFPIFHKIKILGSEGEPAFRFLVDSSKKEPRWNFWKYLVNPEGQVVKFWKPEEPIEVIRPDIAALVRQVIIKKKEDL 209
               SCOP domains d               3cync_ C:       automated matches                                                                                                                                                     SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author h---------------hhhhhhhh.------..hhhh.eee.....eee.hhhh..eeeeeee.....hhhhhhhhhhhhhhhhh...eeeeeee..........hhhhhhhhhhhhhh................hhhhhhhhhhhh........eeee.....eeeee....hhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------R--------------------------- SAPs(SNPs)
                PROSITE (1) ------------------------GLUTATHIONE_PEROXID_3  PDB: C:44-204 UniProt: 37-204                                                                                                                    ----- PROSITE (1)
                PROSITE (2) -------------------------------------------------------------------------------------------GLUTATHI-------------------------------------------------------------------------------------------------- PROSITE (2)
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3cyn C  34 G---------------TENLYFQSM------INSFYAFEVKDAKGRTVSLEKYKGKVSLVVNVASDCQLTDRNYLGLKELHKEFGPSHFSVLAFPCNQFGESEPRPSKEVESFARKNYGVTFPIFHKIKILGSEGEPAFRFLVDSSKKEPRWNFWKYLVNPEGQVVKFWRPEEPIEVIRPDIAALVRQVIIKKKEDL 209
                            |        -      | 38    |    - |      52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       
                           34              35      43     44

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	d3cyna_	A:
1b	d3cynb_	B:
1c	d3cync_	C:

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

(no "Pfam Domain" information available for 3CYN)

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.

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

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	3cyn
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	GPX8_HUMAN \| Q8TED1	:	3kij

(no "Related Entries Specified in the PDB File" available for 3CYN)

Description

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Chains, Units

Ligands, Modified Residues, Ions (2, 9)

Sites (9, 9)

SS Bonds (0, 0)

Cis Peptide Bonds (3, 3)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (1, 3)

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