1RRH - JenaLib

Asym./Biol. Unit (Jmol Viewer)

Asym./Biol. Unit - sites (Jmol Viewer)

Title :   SOYBEAN LIPOXYGENASE (LOX-3) AT AMBIENT TEMPERATURES AT 2.0 A RESOLUTION

Authors :   O. Y. Borbulevych, J. Jankun, E. Skrzypczak-Jankun

Date :   08 Dec 03 (Deposition) - 21 Dec 04 (Release) - 08 Feb 12 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.00

Chains :   Asym./Biol. Unit : A

Keywords :   Oxidoreductase, Iron Metalloprotein, Lipoxygenase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   E. Skrzypczak-Jankun, O. Y. Borbulevych, M. I. Zavodszky, M. R. Baranski, K. Padmanabhan, V. Petricek, J. Jankun
Effect Of Crystal Freezing And Small-Molecule Binding On Internal Cavity Size In A Large Protein: X-Ray And Docking Studies Of Lipoxygenase At Ambient And Low Temperature At 2. 0 A Resolution.
Acta Crystallogr. , Sect. D V. 62 766 2006
PubMed-ID: 16790932 | Reference-DOI: 10.1107/S0907444906016982
(for further references see the PDB file header)

Molecule 1 - SEED LIPOXYGENASE-3
	Chains	:	A
	EC Number	:	1.13.11.12
	Organism Common	:	SOYBEAN
	Organism Scientific	:	GLYCINE MAX
	Organism Taxid	:	3847
	Strain	:	SOYBEAN PROVAR CULTIVAR
	Synonym	:	L-3

		1
Asymmetric/Biological Unit	:	A

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (1, 1)

No.	Name	Count	Type	Full Name
1	FE2	1	Ligand/Ion	FE (II) ION

Asymmetric Unit (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	HIS A:518 , HIS A:523 , HIS A:709 , ILE A:857	BINDING SITE FOR RESIDUE FE2 A 858
2	FE	AUTHOR	HIS A:518 , HIS A:523 , HIS A:709 , ASN A:713 , ILE A:857	NULL

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

Asymmetric/Biological Unit

No.	Residues
1	Phe A:383	-	Pro A:384

Asymmetric/Biological Unit (7, 7)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_LOX3_SOYBN_001 *	H	25	D	LOX3_SOYBN	---	---	A	D	25	D
2	UniProt	VAR_LOX3_SOYBN_002 *	P	57	S	LOX3_SOYBN	---	---	A	S	57	S
3	UniProt	VAR_LOX3_SOYBN_003 *	L	112	P	LOX3_SOYBN	---	---	A	P	112	P
4	UniProt	VAR_LOX3_SOYBN_004 *	V	201	I	LOX3_SOYBN	---	---	A	I	201	I
5	UniProt	VAR_LOX3_SOYBN_005 *	E	382	D	LOX3_SOYBN	---	---	A	D	382	D
6	UniProt	VAR_LOX3_SOYBN_006 *	G	428	D	LOX3_SOYBN	---	---	A	D	428	D
7	UniProt	VAR_LOX3_SOYBN_007 *	A	630	T	LOX3_SOYBN	---	---	A	T	630	T
	* ID not provided by source

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

Asymmetric/Biological Unit (4, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	PLAT	PS50095	PLAT domain profile.	LOX3_SOYBN	38-163	1	A:38-163
2	LIPOXYGENASE_3	PS51393	Lipoxygenase iron-binding catalytic domain profile.	LOX3_SOYBN	166-857	1	A:166-857
3	LIPOXYGENASE_1	PS00711	Lipoxygenases iron-binding region signature 1.	LOX3_SOYBN	513-527	1	A:513-527
4	LIPOXYGENASE_2	PS00081	Lipoxygenases iron-binding region signature 2.	LOX3_SOYBN	540-550	1	A:540-550

(no "Exon" information available for 1RRH)

Asymmetric/Biological 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:850
 aligned with LOX3_SOYBN | P09186 from UniProtKB/Swiss-Prot  Length:857

    Alignment length:850
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357       367       377       387       397       407       417       427       437       447       457       467       477       487       497       507       517       527       537       547       557       567       577       587       597       607       617       627       637       647       657       667       677       687       697       707       717       727       737       747       757       767       777       787       797       807       817       827       837       847       857
           LOX3_SOYBN     8 RGHKIKGTVVLMRKNVLHVNSVTSVGGIIGQGLDLVGSTLDTLTAFLGRPVSLQLISATKADANGKGKLGKATFLEGIITSLPTLGAGQSAFKINFEWDDGSGILGAFYIKNFMQTEFFLVSLTLEDIPNHGSIHFVCNSWIYNAKLFKSDRIFFANQTYLPSETPAPLVKYREEELHNLRGDGTGERKEWERVYDYDVYNDLGDPDKGENHARPVLGGNDTFPYPRRGRTGRKPTRKDPNSESRSNDVYLPRDEAFGHLKSSDFLTYGLKSVSQNVLPLLQSAFDLNFTPREFDSFDEVHGLYSGGIKLPTDIISKISPLPVLKEIFRTDGEQALKFPPPKVIQVSKSAWMTDEEFAREMLAGVNPNLIRCLKEFPPRSKLDSQVYGDHTSQITKEHLEPNLEGLTVDEAIQNKRLFLLGHHDPIMPYLRRINATSTKAYATRTILFLKNDGTLRPLAIELSLPHPQGDQSGAFSQVFLPADEGVESSIWLLAKAYVVVNDSCYHQLVSHWLNTHAVVEPFIIATNRHLSVVHPIYKLLHPHYRDTMNINGLARLSLVNDGGVIEQTFLWGRYSVEMSAVVYKDWVFTDQALPADLIKRGMAIEDPSCPHGIRLVIEDYPYAVDGLEIWDAIKTWVHEYVFLYYKSDDTLREDPELQACWKELVEVGHGDKKNEPWWPKMQTREELVEACAIIIWTASALHAAVNFGQYPYGGLILNRPTLSRRFMPEKGSAEYEELRKNPQKAYLKTITPKFQTLIDLSVIEILSRHASDEVYLGERDNPNWTSDTRALEAFKRFGNKLAQIENKLSERNNDEKLRNRCGPVQMPYTLLLPSSKEGLTFRGIPNSISI 857
               SCOP domains d1rrha2 A:8-167 Plant lipoxigenase                                                                                                                              d1rrha1 A:168-857 Lipoxigenase, C-terminal domain                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  SCOP domains
               CATH domains 1rrhA01 A:8-167 Lipoxygenase-1                                                                                                                                  1rrhA02 A:168-267 Lipoxygenase-1; Domain 2                                                          1rrhA03 A:268-356 Lipoxygenase-1; Domain 3                                               1rrhA04 A:357-490  [code=3.10.450.60, no name defined]                                                                                1rrhA05 A:491-856 Lipoxygenase-1; Domain 5                                                                                                                                                                                                                                                                                                                                    - CATH domains
               Pfam domains --------------------------------------------------PLAT-1rrhA01 A:58-162                                                                                    ----------Lipoxygenase-1rrhA02 A:173-841                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               ---------------- Pfam domains
         Sec.struct. author ..eeeeeeeeeeehhhhhhhhhh...................hhhhh...eeeeeeeeeee.....eee...ee..eee..........eeeeeeeee......eeeeeeee.....eeeeeeeee.......eeeeeeeee.hhhhh...eeee.....hhhhhhhhhhhhhhhhhhhhhh..............ee..........hhhhh..............ee......................hhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhh.........hhhhhhh........hhhhhhhhh...hhhhhhee.....ee...hhhhh...hhhhhhhhhhhhhhhh......ee............hhhhh.................hhhhhhhh..eeeeee...hhhhhhhhh.......eeeeeeee.....eeeeeeeeee....hhhhh.eeeee....hhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eee.......eee....hhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhh.hhhhh.........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.................hhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhh...................hhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhh............................. Sec.struct. author
                 SAPs(SNPs) -----------------D-------------------------------S------------------------------------------------------P----------------------------------------------------------------------------------------I------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------D---------------------------------------------D---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------T----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ------------------------------PLAT  PDB: A:38-163 UniProt: 38-163                                                                                           --LIPOXYGENASE_3  PDB: A:166-857 UniProt: 166-857                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      PROSITE (1)
                PROSITE (2) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------LIPOXYGENASE_1 ------------LIPOXYGENAS------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (2)
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1rrh A   8 RGHKIKGTVVLMRKNVLDVNSVTSVGGIIGQGLDLVGSTLDTLTAFLGRSVSLQLISATKADANGKGKLGKATFLEGIITSLPTLGAGQSAFKINFEWDDGSGIPGAFYIKNFMQTEFFLVSLTLEDIPNHGSIHFVCNSWIYNAKLFKSDRIFFANQTYLPSETPAPLVKYREEELHNLRGDGTGERKEWERIYDYDVYNDLGDPDKGENHARPVLGGNDTFPYPRRGRTGRKPTRKDPNSESRSNDVYLPRDEAFGHLKSSDFLTYGLKSVSQNVLPLLQSAFDLNFTPREFDSFDEVHGLYSGGIKLPTDIISKISPLPVLKEIFRTDGEQALKFPPPKVIQVSKSAWMTDEEFAREMLAGVNPNLIRCLKDFPPRSKLDSQVYGDHTSQITKEHLEPNLEGLTVDEAIQNKRLFLLDHHDPIMPYLRRINATSTKAYATRTILFLKNDGTLRPLAIELSLPHPQGDQSGAFSQVFLPADEGVESSIWLLAKAYVVVNDSCYHQLVSHWLNTHAVVEPFIIATNRHLSVVHPIYKLLHPHYRDTMNINGLARLSLVNDGGVIEQTFLWGRYSVEMSAVVYKDWVFTDQALPADLIKRGMAIEDPSCPHGIRLVIEDYPYTVDGLEIWDAIKTWVHEYVFLYYKSDDTLREDPELQACWKELVEVGHGDKKNEPWWPKMQTREELVEACAIIIWTASALHAAVNFGQYPYGGLILNRPTLSRRFMPEKGSAEYEELRKNPQKAYLKTITPKFQTLIDLSVIEILSRHASDEVYLGERDNPNWTSDTRALEAFKRFGNKLAQIENKLSERNNDEKLRNRCGPVQMPYTLLLPSSKEGLTFRGIPNSISI 857
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357       367       377       387       397       407       417       427       437       447       457       467       477       487       497       507       517       527       537       547       557       567       577       587       597       607       617       627       637       647       657       667       677       687       697       707       717       727       737       747       757       767       777       787       797       807       817       827       837       847       857

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/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: PLAT (25)

Family: PLAT (25)

Glycine max (Soybean) (Glycine hispida) (10)

PLAT-1rrhA01

A:58-162

Clan: no clan defined [family: Lipoxygenase] (13)

Family: Lipoxygenase (13)

Glycine max (Soybean) (Glycine hispida) (10)

Lipoxygenase-1rrhA02

A:173-841

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (LOX3_SOYBN | P09186)

molecular function
	GO:0051213	dioxygenase activity	Catalysis of an oxidation-reduction (redox) reaction in which both atoms of oxygen from one molecule of O2 are incorporated into the (reduced) product(s) of the reaction. The two atoms of oxygen may be distributed between two different products.
	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:0016702	oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen	Catalysis of an oxidation-reduction (redox) reaction in which hydrogen or electrons are transferred from one donor, and two oxygen atoms is incorporated into a donor.
biological process
	GO:0006633	fatty acid biosynthetic process	The chemical reactions and pathways resulting in the formation of a fatty acid, any of the aliphatic monocarboxylic acids that can be liberated by hydrolysis from naturally occurring fats and oils. Fatty acids are predominantly straight-chain acids of 4 to 24 carbon atoms, which may be saturated or unsaturated; branched fatty acids and hydroxy fatty acids also occur, and very long chain acids of over 30 carbons are found in waxes.
	GO:0006631	fatty acid metabolic process	The chemical reactions and pathways involving fatty acids, aliphatic monocarboxylic acids liberated from naturally occurring fats and oils by hydrolysis.
	GO:0006629	lipid metabolic process	The chemical reactions and pathways involving lipids, compounds soluble in an organic solvent but not, or sparingly, in an aqueous solvent. Includes fatty acids; neutral fats, other fatty-acid esters, and soaps; long-chain (fatty) alcohols and waxes; sphingoids and other long-chain bases; glycolipids, phospholipids and sphingolipids; and carotenes, polyprenols, sterols, terpenes and other isoprenoids.
	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:0031408	oxylipin biosynthetic process	The chemical reactions and pathways resulting in the formation of any oxylipin, any of a group of biologically active compounds formed by oxidative metabolism of polyunsaturated fatty acids.
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

Asymmetric/Biological 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
		FE2	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]

	Sites
		AC1	[ RasMol ]	+environment [ RasMol ]
		FE	[ RasMol ]	+environment [ RasMol ]

	Cis Peptide Bonds
		Phe A:383 - Pro A:384	[ RasMol ]

Jmol
	protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick [ Asym./Biol. Unit PNG format \| Asym./Biol. Unit - sites 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
	1rrh
		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
	LOX3_SOYBN \| P09186
		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)
	1.13.11.12
		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
	LOX3_SOYBN \| P09186
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

UniProtKB/Swiss-Prot
	LOX3_SOYBN \| P09186	:	1hu9 1ik3 1jnq 1lnh 1n8q 1no3 1rov 1rrl

1lnh	NATIVE SOYBEAN LIPOXYGENASE (LOX-3) AT 2.6 A RESOLUTION
1no3	SOYBEAN LIPOXYGENASE (LOX-3): 4-NITROCATECHOL
1rrl	SOYBEAN LIPOXYGENASE (LOX-3) AT 93K AT 2.0 A RESOLUTION

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (1, 1)

Sites (2, 2)

SS Bonds (0, 0)

Cis Peptide Bonds (1, 1)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (7, 7)

PROSITE Motifs (4, 4)

Exons (0, 0)

Sequences/Alignments

Classification and Annotation

SCOP Domains (2, 2)

CATH Domains (5, 5)

Pfam Domains (2, 2)

Gene Ontology (10, 10)

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