1QGJ - JenaLib

Asym.Unit - manually (Jmol Viewer)

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)

Title :   ARABIDOPSIS THALIANA PEROXIDASE N

Authors :   O. Mirza, L. Oestergaard, K. G. Welinder, A. Henriksen, M. Gajhede

Date :   29 Apr 99 (Deposition) - 08 Mar 00 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.90

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

Keywords :   Peroxidase, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   O. Mirza, A. Henriksen, L. Ostergaard, K. G. Welinder, M. Gajhede
Arabidopsis Thaliana Peroxidase N: Structure Of A Novel Neutral Peroxidase.
Acta Crystallogr. , Sect. D V. 56 372 2000
PubMed-ID: 10713531 | Reference-DOI: 10.1107/S0907444999016340
(for further references see the PDB file header)

Molecule 1 - PEROXIDASE N
	Chains	:	A, B
	EC Number	:	1.11.1.-
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Organism Common	:	THALE CRESS
	Organism Scientific	:	ARABIDOPSIS THALIANA
	Organism Taxid	:	3702

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (3, 8)

No.	Name	Count	Type	Full Name
1	CA	4	Ligand/Ion	CALCIUM ION
2	GSH	2	Ligand/Ion	GLUTATHIONE
3	HEM	2	Ligand/Ion	PROTOPORPHYRIN IX CONTAINING FE

Biological Unit 1 (2, 2)

No.	Name	Count	Type	Full Name
1	CA	-1	Ligand/Ion	CALCIUM ION
2	GSH	1	Ligand/Ion	GLUTATHIONE
3	HEM	1	Ligand/Ion	PROTOPORPHYRIN IX CONTAINING FE

Biological Unit 2 (2, 2)

No.	Name	Count	Type	Full Name
1	CA	-1	Ligand/Ion	CALCIUM ION
2	GSH	1	Ligand/Ion	GLUTATHIONE
3	HEM	1	Ligand/Ion	PROTOPORPHYRIN IX CONTAINING FE

Asymmetric Unit (8, 8)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ASP A:43 , VAL A:46 , GLY A:48 , ASP A:50 , SER A:52 , HOH A:2012	BINDING SITE FOR RESIDUE CA A 2001
2	AC2	SOFTWARE	THR A:166 , ASP A:217 , THR A:220 , THR A:223 , ASP A:225	BINDING SITE FOR RESIDUE CA A 2002
3	AC3	SOFTWARE	ASP B:43 , VAL B:46 , GLY B:48 , ASP B:50 , SER B:52 , HOH B:2335	BINDING SITE FOR RESIDUE CA B 2001
4	AC4	SOFTWARE	THR B:166 , ASP B:217 , THR B:220 , THR B:223 , ASP B:225	BINDING SITE FOR RESIDUE CA B 2002
5	AC5	SOFTWARE	ARG A:31 , ALA A:34 , SER A:35 , ARG A:38 , PHE A:41 , SER A:70 , ARG A:72 , PRO A:135 , SER A:136 , PRO A:137 , LEU A:161 , SER A:162 , ALA A:164 , HIS A:165 , PHE A:167 , GLY A:168 , GLN A:169 , ALA A:170 , LYS A:171 , SER A:241 , HOH A:2049 , HOH A:2065 , HOH A:2171 , HOH A:2525	BINDING SITE FOR RESIDUE HEM A 1350
6	AC6	SOFTWARE	ARG B:31 , ALA B:34 , SER B:35 , ARG B:38 , PHE B:41 , SER B:70 , ARG B:72 , PRO B:135 , SER B:136 , PRO B:137 , LEU B:161 , SER B:162 , ALA B:164 , HIS B:165 , PHE B:167 , GLY B:168 , GLN B:169 , ALA B:170 , LYS B:171 , SER B:241 , HOH B:2023 , HOH B:2122 , HOH B:2530	BINDING SITE FOR RESIDUE HEM B 1350
7	AC7	SOFTWARE	ASN A:154 , THR A:156 , ASP A:157 , CYS A:275 , ALA A:276 , ARG A:279 , LYS B:27 , ALA B:28 , HOH B:2292	BINDING SITE FOR RESIDUE GSH A 1794
8	AC8	SOFTWARE	THR B:156 , ASP B:157 , CYS B:275 , ALA B:276 , ARG B:279 , HOH B:2177 , HOH B:2238 , HOH B:2322	BINDING SITE FOR RESIDUE GSH B 1794

Asymmetric Unit

No.	Residues
1	A:11	-	A:88
2	A:44	-	A:49
3	A:94	-	A:295
4	A:172	-	A:204
5	B:11	-	B:88
6	B:44	-	B:49
7	B:94	-	B:295
8	B:172	-	B:204

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

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

Asymmetric Unit (3, 6)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	PEROXIDASE_4	PS50873	Plant heme peroxidase family profile.	PER59_ARATH	29-327	2	A:1-299 B:1-299
2	PEROXIDASE_2	PS00436	Peroxidases active site signature.	PER59_ARATH	61-72	2	A:33-44 B:33-44
3	PEROXIDASE_1	PS00435	Peroxidases proximal heme-ligand signature.	PER59_ARATH	185-195	2	A:157-167 B:157-167

Biological Unit 1 (3, 3)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	PEROXIDASE_4	PS50873	Plant heme peroxidase family profile.	PER59_ARATH	29-327	1	A:1-299 -
2	PEROXIDASE_2	PS00436	Peroxidases active site signature.	PER59_ARATH	61-72	1	A:33-44 -
3	PEROXIDASE_1	PS00435	Peroxidases proximal heme-ligand signature.	PER59_ARATH	185-195	1	A:157-167 -

Biological Unit 2 (3, 3)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	PEROXIDASE_4	PS50873	Plant heme peroxidase family profile.	PER59_ARATH	29-327	1	- B:1-299
2	PEROXIDASE_2	PS00436	Peroxidases active site signature.	PER59_ARATH	61-72	1	- B:33-44
3	PEROXIDASE_1	PS00435	Peroxidases proximal heme-ligand signature.	PER59_ARATH	185-195	1	- B:157-167

(no "Exon" information available for 1QGJ)

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:300
 aligned with PER59_ARATH | Q39034 from UniProtKB/Swiss-Prot  Length:328

    Alignment length:300
                                    38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328
          PER59_ARATH    29 QLSPDIYAKSCPNLVQIVRKQVAIALKAEIRMAASLIRLHFHDCFVNGCDASLLLDGADSEKLAIPNINSARGFEVIDTIKAAVENACPGVVSCADILTLAARDSVVLSGGPGWRVALGRKDGLVANQNSANNLPSPFEPLDAIIAKFVAVNLNITDVVALSGAHTFGQAKCAVFSNRLFNFTGLGNPDATLETSLLSNLQTVCPLGGNSNITAPLDRSTTDTFDNNYFKNLLEGKGLLSSDQILFSSDLAVNTTKKLVEAYSRSQSLFFRDFTCAMIRMGNISNGASGEVRTNCRVINN 328
               SCOP domains d1qgja_ A: Plant peroxidase                                                                                                                                                                                                                                                                                  SCOP domains
               CATH domains -1qgjA01 A:2-134,A:281-299  [code=1.10.520.10, no name defined]                                                                       1qgjA02 A:135-280 Peroxidase, domain 2                                                                                                            1qgjA01            - CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .............hhhhhhhhhhhhhhh.hhhhhhhhhhhhhhh.......hhh......hhh..........hhhhhhhhhhhhhh......hhhhhhhhhhhhhhhh..................hhhhhh.......hhhhhhhhhhh...hhhhhhhhhhhh..eeehhh.hhh...............hhhhhhhhhh.........eee..........hhhhhhhhh.....hhhhhhhh...hhh..hhhhhhhhh.hhhhhhhhhhhhhhhhh.................. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                PROSITE (1) PEROXIDASE_4  PDB: A:1-299 UniProt: 29-327                                                                                                                                                                                                                                                                 - PROSITE (1)
                PROSITE (2) --------------------------------PEROXIDASE_2----------------------------------------------------------------------------------------------------------------PEROXIDASE_------------------------------------------------------------------------------------------------------------------------------------- PROSITE (2)
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1qgj A   1 QLSPDIYAKSCPNLVQIVRKQVAIALKAEIRMAASLIRLHFHDCFVNGCDASLLLDGADSEKLAIPNINSARGFEVIDTIKAAVENACPGVVSCADILTLAARDSVVLSGGPGWRVALGRKDGLVANQNSANNLPSPFEPLDAIIAKFVAVNLNITDVVALSGAHTFGQAKCAVFSNRLFNFTGAGNPDATLETSLLSNLQTVCPLGGNSNITAPLDRSTTDTFDNNYFKNLLEGKGLLSSDQILFSSDLAVNTTKKLVEAYSRSQSLFFRDFTCAMIRMGNISNGASGEVRTNCRVINN 300
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300

Chain B from PDB  Type:PROTEIN  Length:300
 aligned with PER59_ARATH | Q39034 from UniProtKB/Swiss-Prot  Length:328

    Alignment length:300
                                    38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328
          PER59_ARATH    29 QLSPDIYAKSCPNLVQIVRKQVAIALKAEIRMAASLIRLHFHDCFVNGCDASLLLDGADSEKLAIPNINSARGFEVIDTIKAAVENACPGVVSCADILTLAARDSVVLSGGPGWRVALGRKDGLVANQNSANNLPSPFEPLDAIIAKFVAVNLNITDVVALSGAHTFGQAKCAVFSNRLFNFTGLGNPDATLETSLLSNLQTVCPLGGNSNITAPLDRSTTDTFDNNYFKNLLEGKGLLSSDQILFSSDLAVNTTKKLVEAYSRSQSLFFRDFTCAMIRMGNISNGASGEVRTNCRVINN 328
               SCOP domains d1qgjb_ B: Plant peroxidase                                                                                                                                                                                                                                                                                  SCOP domains
               CATH domains -1qgjB01 B:2-134,B:281-297  [code=1.10.520.10, no name defined]                                                                       1qgjB02 B:135-280 Peroxidase, domain 2                                                                                                            1qgjB01          --- CATH domains
           Pfam domains (1) -----------------peroxidase-1qgjB01 B:18-265                                                                                                                                                                                                                             ----------------------------------- Pfam domains (1)
           Pfam domains (2) -----------------peroxidase-1qgjB02 B:18-265                                                                                                                                                                                                                             ----------------------------------- Pfam domains (2)
         Sec.struct. author .............hhhhhhhhhhhhhhh.hhhhhhhhhhhhhhh.......hhh......hhh..........hhhhhhhhhhhhhh......hhhhhhhhhhhhhhhh..................hhhhhh.......hhhhhhhhhhh...hhhhhhhhhhhh..eeehhh.hhh...............hhhhhhhhhh.........eee..........hhhhhhhhh.....hhhhhhhh.......hhhhhhhhhh.hhhhhhhhhhhhhhhhh.................. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                PROSITE (1) PEROXIDASE_4  PDB: B:1-299 UniProt: 29-327                                                                                                                                                                                                                                                                 - PROSITE (1)
                PROSITE (2) --------------------------------PEROXIDASE_2----------------------------------------------------------------------------------------------------------------PEROXIDASE_------------------------------------------------------------------------------------------------------------------------------------- PROSITE (2)
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1qgj B   1 QLSPDIYAKSCPNLVQIVRKQVAIALKAEIRMAASLIRLHFHDCFVNGCDASLLLDGADSEKLAIPNINSARGFEVIDTIKAAVENACPGVVSCADILTLAARDSVVLSGGPGWRVALGRKDGLVANQNSANNLPSPFEPLDAIIAKFVAVNLNITDVVALSGAHTFGQAKCAVFSNRLFNFTGAGNPDATLETSLLSNLQTVCPLGGNSNITAPLDRSTTDTFDNNYFKNLLEGKGLLSSDQILFSSDLAVNTTKKLVEAYSRSQSLFFRDFTCAMIRMGNISNGASGEVRTNCRVINN 300
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300

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: All alpha proteins (14657)

Fold: Heme-dependent peroxidases (402)

Superfamily: Heme-dependent peroxidases (402)

Family: CCP-like (292)

Protein domain: Plant peroxidase (35)

Thale cress (Arabidopsis thaliana), peroxidase N [TaxId: 3702] (1)

1a	d1qgja_	A:
1b	d1qgjb_	B:

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Mainly Alpha (13335)

Architecture: Orthogonal Bundle (10391)

Topology: Peroxidase; domain 1 (244)

Homologous Superfamily: [code=1.10.520.10, no name defined] (241)

Thale cress (Arabidopsis thaliana) (2)

1a	1qgjA01	A:2-134,A:281-299
1b	1qgjB01	B:2-134,B:281-297

Topology: Peroxidase; domain 2 (241)

Homologous Superfamily: Peroxidase, domain 2 (241)

Thale cress (Arabidopsis thaliana) (2)

2a	1qgjA02	A:135-280
2b	1qgjB02	B:135-280

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: no clan defined [family: peroxidase] (92)

Family: peroxidase (92)

Arabidopsis thaliana (Mouse-ear cress) (3)

1a	peroxidase-1qgjB01	B:18-265
1b	peroxidase-1qgjB02	B:18-265

Asymmetric Unit(hide GO term definitions)

Chain A,B (PER59_ARATH | Q39034)

molecular function
	GO:0020037	heme binding	Interacting selectively and non-covalently with heme, any compound of iron complexed in a porphyrin (tetrapyrrole) ring.
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	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:0042744	hydrogen peroxide catabolic process	The chemical reactions and pathways resulting in the breakdown of hydrogen peroxide (H2O2).
	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.
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	GO:0005576	extracellular region	The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.
	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.

Asymmetric Unit
	Complete Structure
		Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
		WebMol \| AstexViewer[tm]@PDBe (Java Applets, require no local installation except for Java; loading may be slow)
		STRAP (Java WebStart application, automatic local installation, requires Java; full application with system access!)
		RasMol (require local installation)
		Molscript (VRML) (requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)

	Ligands, Modified Residues, Ions
		CA	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		GSH	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		HEM	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]

	Sites
		AC1	[ RasMol ]	+environment [ RasMol ]
		AC2	[ RasMol ]	+environment [ RasMol ]
		AC3	[ RasMol ]	+environment [ RasMol ]
		AC4	[ RasMol ]	+environment [ RasMol ]
		AC5	[ RasMol ]	+environment [ RasMol ]
		AC6	[ RasMol ]	+environment [ RasMol ]
		AC7	[ RasMol ]	+environment [ RasMol ]
		AC8	[ RasMol ]	+environment [ RasMol ]

	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 1qgj)

Biological Units
	Complete Structure
		Biological Unit 1	[ Jena3D ]
		Biological Unit 2	[ Jena3D ]

Jmol
	protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick [ Asym. Unit PNG format \| Asym. Unit - sites PNG format \| Biol. Unit 1 PNG format \| Biol. Unit 1 - sites PNG format \| Biol. Unit 2 PNG format ](automatic orientation, automatically generated)
Molscript
	protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick [ mono PDF format \| stereo PDF format ](default orientation, automatically generated)

Access by PDB/NDB ID
	1qgj
		Family and Domain Information	:	ProDom \| SYSTERS
		General Structural Information	:	GlycoscienceDB \| MMDB \| NDB \| OCA \| PDB \| PDBe \| PDBj \| PDBsum \| PDBWiki \| PQS \| PROTEOPEDIA
		Orientation in Membranes	:	OPM
		Protein Surface	:	SURFACE
		Secondary Structure	:	DSSP (structure derived) \| HSSP (homology derived)
		Structural Genomics	:	GeneCensus
		Structural Neighbours	:	CE \| VAST
		Structure Classification	:	CATH \| Dali \| SCOP
		Validation and Original Data	:	BMRB Data View \| BMRB Restraints Grid \| EDS \| PROCHECK \| RECOORD \| WHAT_CHECK

Access by UniProt ID/Accession number
	PER59_ARATH \| Q39034
		Comparative Protein Structure Models	:	ModBase
		Genomic Information	:	Ensembl
		Protein-protein Interaction	:	DIP
		Sequence, Family and Domain Information	:	InterPro \| Pfam \| SMART \| UniProtKB/SwissProt

Access by Enzyme Classificator (EC Number)
	1.11.1.-
		General Enzyme Information	:	BRENDA \| EC-PDB \| Enzyme \| IntEnz
		Pathway	:	KEGG \| MetaCyc

Access by Disease Identifier (MIM ID)
	(no 'MIM ID' available)
		Disease Information	:	OMIM

Access by GenAge ID
	(no 'GenAge ID' available)
		Age Related Information	:	GenAge

Access by PDB/NDB ID
		Domain Information	:	XDom
		Interatomic Contacts of Structural Units	:	CSU
		Ligand-protein Contacts	:	LPC
		Protein Cavities	:	castP
		Sequence and Secondary Structure	:	PDBCartoon
		Structure Alignment	:	STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
		Structure and Sequence Browser	:	STING

Access by UniProt ID/Accession number
	PER59_ARATH \| Q39034
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

(no "Entries Sharing at Least One Protein Chain" available for 1QGJ)

(no "Related Entries Specified in the PDB File" available for 1QGJ)

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 8)

Sites (8, 8)

SS Bonds (8, 8)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (3, 6)

Exons (0, 0)

Sequences/Alignments

Classification and Annotation

SCOP Domains (1, 2)

CATH Domains (2, 4)

Pfam Domains (1, 2)

Gene Ontology (11, 11)

Visualization

Interactive Views

Still Images

Databases and Analysis Tools

Databases

Analysis Tools

Related Entries

Entries Sharing at Least One Protein Chain (UniProt ID)

Related Entries Specified in the PDB File