1NO3 - JenaLib

Asym./Biol. Unit (Jmol Viewer)

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Title :   REFINED STRUCTURE OF SOYBEAN LIPOXYGENASE-3 WITH 4-NITROCATECHOL AT 2.15 ANGSTROM RESOLUTION

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

Date :   15 Jan 03 (Deposition) - 03 Jun 03 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.15

Chains :   Asym./Biol. Unit : A

Keywords :   Lipoxygenase, 4-Nitrocatechol, Iron, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   E. Skrzypczak-Jankun, O. Y. Borbulevych, J. Jankun
Soybean Lipoxygenase-3 In Complex With 4-Nitrocatechol.
Acta Crystallogr. , Sect. D V. 60 613 2004
PubMed-ID: 14993710 | Reference-DOI: 10.1107/S0907444904000861
(for further references see the PDB file header)

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

		1
Asymmetric/Biological Unit	:	A

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (2, 2)

No.	Name	Count	Type	Full Name
1	4NC	1	Ligand/Ion	4-NITROCATECHOL
2	FE	1	Ligand/Ion	FE (III) ION

Asymmetric Unit (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	HIS A:518 , HIS A:523 , HIS A:709 , ASN A:713 , ILE A:857 , HOH A:1533	BINDING SITE FOR RESIDUE FE A 858
2	AC2	SOFTWARE	GLN A:514 , HIS A:518 , TRP A:519 , HIS A:523 , ILE A:557 , LEU A:565 , ILE A:572 , LEU A:773 , ILE A:857	BINDING SITE FOR RESIDUE 4NC A 859

(no "SS Bond" information available for 1NO3)

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 1NO3)

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:851
 aligned with LOX3_SOYBN | P09186 from UniProtKB/Swiss-Prot  Length:857

    Alignment length:851
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       356       366       376       386       396       406       416       426       436       446       456       466       476       486       496       506       516       526       536       546       556       566       576       586       596       606       616       626       636       646       656       666       676       686       696       706       716       726       736       746       756       766       776       786       796       806       816       826       836       846       856 
           LOX3_SOYBN     7 HRGHKIKGTVVLMRKNVLHVNSVTSVGGIIGQGLDLVGSTLDTLTAFLGRPVSLQLISATKADANGKGKLGKATFLEGIITSLPTLGAGQSAFKINFEWDDGSGILGAFYIKNFMQTEFFLVSLTLEDIPNHGSIHFVCNSWIYNAKLFKSDRIFFANQTYLPSETPAPLVKYREEELHNLRGDGTGERKEWERVYDYDVYNDLGDPDKGENHARPVLGGNDTFPYPRRGRTGRKPTRKDPNSESRSNDVYLPRDEAFGHLKSSDFLTYGLKSVSQNVLPLLQSAFDLNFTPREFDSFDEVHGLYSGGIKLPTDIISKISPLPVLKEIFRTDGEQALKFPPPKVIQVSKSAWMTDEEFAREMLAGVNPNLIRCLKEFPPRSKLDSQVYGDHTSQITKEHLEPNLEGLTVDEAIQNKRLFLLGHHDPIMPYLRRINATSTKAYATRTILFLKNDGTLRPLAIELSLPHPQGDQSGAFSQVFLPADEGVESSIWLLAKAYVVVNDSCYHQLVSHWLNTHAVVEPFIIATNRHLSVVHPIYKLLHPHYRDTMNINGLARLSLVNDGGVIEQTFLWGRYSVEMSAVVYKDWVFTDQALPADLIKRGMAIEDPSCPHGIRLVIEDYPYAVDGLEIWDAIKTWVHEYVFLYYKSDDTLREDPELQACWKELVEVGHGDKKNEPWWPKMQTREELVEACAIIIWTASALHAAVNFGQYPYGGLILNRPTLSRRFMPEKGSAEYEELRKNPQKAYLKTITPKFQTLIDLSVIEILSRHASDEVYLGERDNPNWTSDTRALEAFKRFGNKLAQIENKLSERNNDEKLRNRCGPVQMPYTLLLPSSKEGLTFRGIPNSISI 857
               SCOP domains d1no3a2 A:7-167 Plant lipoxigenase                                                                                                                               d1no3a1 A:168-857 Lipoxigenase, C-terminal domain                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  SCOP domains
               CATH domains --1no3A01 A:9-167 Lipoxygenase-1                                                                                                                                 1no3A02 A:168-267 Lipoxygenase-1; Domain 2                                                          1no3A03 A:268-356 Lipoxygenase-1; Domain 3                                               1no3A04 A:357-490  [code=3.10.450.60, no name defined]                                                                                1no3A05 A:491-856 Lipoxygenase-1; Domain 5                                                                                                                                                                                                                                                                                                                                    - CATH domains
               Pfam domains ---------------------------------------------------PLAT-1no3A01 A:58-162                                                                                    ----------Lipoxygenase-1no3A02 A:173-841                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               ---------------- Pfam domains
         Sec.struct. author ...eeeeeeeeeeehhhhhhhhhh..................hhhhhh...eeeeeeeeeee.....eee...ee..eee.........eeeeeeeeee......eeeeeeee.....eeeeeeeee.......eeeeeeeee.hhhhh...eeee.....hhhhhhhhhhhhhhhhhhhhhh..............ee......hhhhhhhhh..............ee......................hhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhh.........hhhhhhhhhh.....hhhhhhhhh...hhhhhh............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
                 1no3 A   7 HRGHKIKGTVVLMRKNVLDVNSVTSVGGIIGQGLDLVGSTLDTLTAFLGRSVSLQLISATKADANGKGKLGKATFLEGIITSLPTLGAGQSAFKINFEWDDGSGIPGAFYIKNFMQTEFFLVSLTLEDIPNHGSIHFVCNSWIYNAKLFKSDRIFFANQTYLPSETPAPLVKYREEELHNLRGDGTGERKEWERIYDYDVYNDLGDPDKGENHARPVLGGNDTFPYPRRGRTGRKPTRKDPNSESRSNDVYLPRDEAFGHLKSSDFLTYGLKSVSQNVLPLLQSAFDLNFTPREFDSFDEVHGLYSGGIKLPTDIISKISPLPVLKEIFRTDGEQALKFPPPKVIQVSKSAWMTDEEFAREMLAGVNPNLIRCLKDFPPRSKLDSQVYGDHTSQITKEHLEPNLEGLTVDEAIQNKRLFLLDHHDPIMPYLRRINATSTKAYATRTILFLKNDGTLRPLAIELSLPHPQGDQSGAFSQVFLPADEGVESSIWLLAKAYVVVNDSCYHQLVSHWLNTHAVVEPFIIATNRHLSVVHPIYKLLHPHYRDTMNINGLARLSLVNDGGVIEQTFLWGRYSVEMSAVVYKDWVFTDQALPADLIKRGMAIEDPSCPHGIRLVIEDYPYTVDGLEIWDAIKTWVHEYVFLYYKSDDTLREDPELQACWKELVEVGHGDKKNEPWWPKMQTREELVEACAIIIWTASALHAAVNFGQYPYGGLILNRPTLSRRFMPEKGSAEYEELRKNPQKAYLKTITPKFQTLIDLSVIEILSRHASDEVYLGERDNPNWTSDTRALEAFKRFGNKLAQIENKLSERNNDEKLRNRCGPVQMPYTLLLPSSKEGLTFRGIPNSISI 857
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       356       366       376       386       396       406       416       426       436       446       456       466       476       486       496       506       516       526       536       546       556       566       576       586       596       606       616       626       636       646       656       666       676       686       696       706       716       726       736       746       756       766       776       786       796       806       816       826       836       846       856

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-1no3A01

A:58-162

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

Family: Lipoxygenase (13)

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

Lipoxygenase-1no3A02

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

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	1no3
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	LOX3_SOYBN \| P09186
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	1.13.11.12
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	LOX3_SOYBN \| P09186
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UniProtKB/Swiss-Prot
	LOX3_SOYBN \| P09186	:	1hu9 1ik3 1jnq 1lnh 1n8q 1rov 1rrh 1rrl

1byt	UNREFINED MODEL OF SOYBEAN LIPOXYGENASE-3 WITH 4- NITROCATECHOL
1n8q	COMPLEX OF SOYBEAN LIPOXYGENASE-3 WITH PROTOCATECHUIC ACID

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 2)

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

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SCOP Domains (2, 2)

CATH Domains (5, 5)

Pfam Domains (2, 2)

Gene Ontology (10, 10)

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