3VF1 - JenaLib

Title :   STRUCTURE OF A CALCIUM-DEPENDENT 11R-LIPOXYGENASE SUGGESTS A MECHANISM FOR CA-REGULATION

Authors :   P. Eek, R. Jarving, I. Jarving, N. C. Gilbert, M. E. Newcomer, N. Samel

Date :   09 Jan 12 (Deposition) - 16 May 12 (Release) - 25 Jul 12 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.47

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

Keywords :   Lox, Plat, Beta Sandwich, C2-Like Domain, Non-Heme Iron, Conformational Change, Dioxygenase, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   P. Eek, R. Jarving, I. Jarving, N. C. Gilbert, M. E. Newcomer, N. Samel
Structure Of A Calcium-Dependent 11R-Lipoxygenase Suggests Mechanism For Ca2+ Regulation.
J. Biol. Chem. V. 287 22377 2012
PubMed-ID: 22573333 | Reference-DOI: 10.1074/JBC.M112.343285

Compounds

Molecule 1 - 11R-LIPOXYGENASE
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET11A
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Organism Scientific	:	GERSEMIA FRUTICOSA
	Organism Taxid	:	134440

Structural Features

Chains, Units

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

Summary Information (see also Sequences/Alignments below)

Ligands, Modified Residues, Ions (2, 4)

Asymmetric Unit (2, 4)

No.	Name	Count	Type	Full Name
1	FE2	2	Ligand/Ion	FE (II) ION
2	SUC	2	Ligand/Ion	SUCROSE

Biological Unit 1 (2, 2)

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

Biological Unit 2 (2, 2)

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

Sites (4, 4)

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	HIS A:373 , HIS A:378 , HIS A:556 , ASN A:560 , ILE A:679 , HOH A:942	BINDING SITE FOR RESIDUE FE2 A 701
2	AC2	SOFTWARE	ASP A:466 , GLY A:467 , ARG A:469 , LYS A:474 , ASP A:475 , LEU A:478 , HOH A:848 , HOH A:931 , HOH A:935	BINDING SITE FOR RESIDUE SUC A 702
3	AC3	SOFTWARE	HIS B:373 , HIS B:378 , HIS B:556 , ASN B:560 , ILE B:679	BINDING SITE FOR RESIDUE FE2 B 701
4	AC4	SOFTWARE	ARG B:461 , ASP B:466 , GLY B:467 , LEU B:468 , LYS B:474 , ASP B:475 , LEU B:478 , HOH B:830 , HOH B:839 , HOH B:952 , HOH B:998	BINDING SITE FOR RESIDUE SUC B 702

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

Sequences/Alignments

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:680
 aligned with Q2N410_9CNID | Q2N410 from UniProtKB/TrEMBL  Length:679

    Alignment length:680
                             1                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       359       369       379       389       399       409       419       429       439       449       459       469       479       489       499       509       519       529       539       549       559       569       579       589       599       609       619       629       639       649       659       669       679
         Q2N410_9CNID     - -MKYKITVETGDLRGAGTDASVSIKLTGKDGAETSAFSLDKDFHNDFESGGTDTYDQSGVDVGEIAMITLKENGFGLKSDWYIAKVIIEKIDEATGFSNKYIFPCYRWVIKQLVVYEGKAILPNSKDNVKTIAEQRTKEVSENKKLYKWGTDPRYVQDLPGFVDAEEPKSLPKDVQFTDEATSSLFRVGLADFANLGLSHLFGIWDDWDCLEDFRQLITPAIKSGLPHAAEYWRDDVWFGSQFLNGSNPEVIRRCDKLPENFPVKNEMVEKLLDRGYTLEKAMKEGLIFITDYKILEGIPTMDTPEDKRYITTPLGLFYLKNNDDIIPIAIQLYQQPGENNSIWTPLKDTEWDWIMAKLWLRCADTQYHQMITHLLRCHLMMEPTAVSSWRNLPSVHPVWKLLYPHTKGIMAINTLGRNDLIPTGGAADKVLSIGGGGQVTLMQKHYRSVTFDSYDLVKDLRQRGVDGLRKFYYKDDALLLWNVIHQFVQDIIQIYYNDDDSVKKDNEIQDWIRDLHENGYPAGSDGTDKKVPKSFENREELVHFLTVVVFTCSCQHAAVNFSQMATYGFHPNSPTLMRQPPPTEKGKSNHKVIMASLANKHQAVTMVSVVNALTTIYPTEKFLGDYADNLFGDAAAHAAMAKFKSNLANITKQITERNQGMVSPYTWLIPGHVPNSIAI 679
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeeee...........eeeeeee........eee............eeeeeeee.....eeeeeeee.........eeeeeeeeee......eeeeeeeeeee...eeeee............hhhhhhhhhhhhhhhhhhh....hhhhh..........hhhhhhhhhh..hhhhhhh...hhhhhhhhhhhhhh.......hhhhhhhhh.........hhhhhh.hhhhhhhhhhhh......ee..........hhhhhhhhh....hhhhhhhh..eeeee.hhhh.....ee..ee......eeeeee.....eeeeeee..........ee.....hhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhh..................hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...............hhhhhhhhh.hhhhhhhhhhhhhhhh..................hhhhhhhhhhhhhhhhhhhhhhhhhh..........hhhhh...... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3vf1 A   0 HMKYKITVETGDLRGAGTDASVSIKLTGKDGAETSAFSLDKYFHNDFESGGTDTYDQSGVDVGEIAMITLKENGFGLKSDWYIAKVIIEKIDEATGFSNKYIFPCYRWVIKQLVVYEGKAILPNSKDNVKTIAEQRTKEVSENKKLYKWGTDPRYVQDLPGFVDAEEPKSLPKDVQFTDEATSSLFRVGLADFANLGLSHLFGIWDDWDCLEDFRQLITPAIKSGLPHAAEYWRDDVWFGSQFLNGSNPEVIRRCDKLPENFPVKNEMVEKLLDRGYTLEKAMKEGLIFITDYKILEGIPTMDTPEDKRYITTPLGLFYLKNNDDIIPIAIQLYQQPGENNSIWTPLKDTEWDWIMAKLWLRCADTQYHQMITHLLRCHLMMEPTAVSSWRNLPSVHPVWKLLYPHTKGIMAINTLGRNDLIPTGGAADKVLSIGGGGQVTLMQKHYRSVTFDSYDLVKDLRQRGVDGLRKFYYKDDALLLWNVIHQFVQDIIQIYYNDDDSVKKDNEIQDWIRDLHENGYPAGSDGTDKKVPKSFENREELVHFLTVVVFTCSCQHAAVNFSQMATYGFHPNSPTLMRQPPPTEKGKSNHKVIMASLANKHQAVTMVSVVNALTTIYPTEKFLGDYADNLFGDAAAHAAMAKFKSNLANITKQITERNQGMVSPYTWLIPGHVPNSIAI 679
                                     9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       359       369       379       389       399       409       419       429       439       449       459       469       479       489       499       509       519       529       539       549       559       569       579       589       599       609       619       629       639       649       659       669       679

Chain B from PDB  Type:PROTEIN  Length:680
 aligned with Q2N410_9CNID | Q2N410 from UniProtKB/TrEMBL  Length:679

    Alignment length:680
                             1                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       359       369       379       389       399       409       419       429       439       449       459       469       479       489       499       509       519       529       539       549       559       569       579       589       599       609       619       629       639       649       659       669       679
         Q2N410_9CNID     - -MKYKITVETGDLRGAGTDASVSIKLTGKDGAETSAFSLDKDFHNDFESGGTDTYDQSGVDVGEIAMITLKENGFGLKSDWYIAKVIIEKIDEATGFSNKYIFPCYRWVIKQLVVYEGKAILPNSKDNVKTIAEQRTKEVSENKKLYKWGTDPRYVQDLPGFVDAEEPKSLPKDVQFTDEATSSLFRVGLADFANLGLSHLFGIWDDWDCLEDFRQLITPAIKSGLPHAAEYWRDDVWFGSQFLNGSNPEVIRRCDKLPENFPVKNEMVEKLLDRGYTLEKAMKEGLIFITDYKILEGIPTMDTPEDKRYITTPLGLFYLKNNDDIIPIAIQLYQQPGENNSIWTPLKDTEWDWIMAKLWLRCADTQYHQMITHLLRCHLMMEPTAVSSWRNLPSVHPVWKLLYPHTKGIMAINTLGRNDLIPTGGAADKVLSIGGGGQVTLMQKHYRSVTFDSYDLVKDLRQRGVDGLRKFYYKDDALLLWNVIHQFVQDIIQIYYNDDDSVKKDNEIQDWIRDLHENGYPAGSDGTDKKVPKSFENREELVHFLTVVVFTCSCQHAAVNFSQMATYGFHPNSPTLMRQPPPTEKGKSNHKVIMASLANKHQAVTMVSVVNALTTIYPTEKFLGDYADNLFGDAAAHAAMAKFKSNLANITKQITERNQGMVSPYTWLIPGHVPNSIAI 679
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeeee...........eeeeeee........eee............eeeeeeee.....eeeeeeee.........eeeeeeeeee......eeeeeeeeeee...eeeee............hhhhhhhhhhhhhhhhhhh....hhhhh..........hhhhhhhhhh..hhhhhhh...hhhhhhhhhhhhhh.......hhhhhhhhh.........hhhhhh.hhhhhhhhhhhh......ee..........hhhhhhhhh....hhhhhhhh..eeeee.hhhh.....ee..ee......eeeeee.....eeeeeee..........ee.....hhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhh..................hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...............hhhhhhhhh.hhhhhhhhhhhhhhhh..................hhhhhhhhhhhhhhhhhhhhhhhhhh..........hhhhh...... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3vf1 B   0 HMKYKITVETGDLRGAGTDASVSIKLTGKDGAETSAFSLDKYFHNDFESGGTDTYDQSGVDVGEIAMITLKENGFGLKSDWYIAKVIIEKIDEATGFSNKYIFPCYRWVIKQLVVYEGKAILPNSKDNVKTIAEQRTKEVSENKKLYKWGTDPRYVQDLPGFVDAEEPKSLPKDVQFTDEATSSLFRVGLADFANLGLSHLFGIWDDWDCLEDFRQLITPAIKSGLPHAAEYWRDDVWFGSQFLNGSNPEVIRRCDKLPENFPVKNEMVEKLLDRGYTLEKAMKEGLIFITDYKILEGIPTMDTPEDKRYITTPLGLFYLKNNDDIIPIAIQLYQQPGENNSIWTPLKDTEWDWIMAKLWLRCADTQYHQMITHLLRCHLMMEPTAVSSWRNLPSVHPVWKLLYPHTKGIMAINTLGRNDLIPTGGAADKVLSIGGGGQVTLMQKHYRSVTFDSYDLVKDLRQRGVDGLRKFYYKDDALLLWNVIHQFVQDIIQIYYNDDDSVKKDNEIQDWIRDLHENGYPAGSDGTDKKVPKSFENREELVHFLTVVVFTCSCQHAAVNFSQMATYGFHPNSPTLMRQPPPTEKGKSNHKVIMASLANKHQAVTMVSVVNALTTIYPTEKFLGDYADNLFGDAAAHAAMAKFKSNLANITKQITERNQGMVSPYTWLIPGHVPNSIAI 679
                                     9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       359       369       379       389       399       409       419       429       439       449       459       469       479       489       499       509       519       529       539       549       559       569       579       589       599       609       619       629       639       649       659       669       679

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 '\|'

Classification and Annotation

SCOP Domains (0, 0)

CATH Domains (0, 0)

Pfam Domains (0, 0)

Gene Ontology (6, 6)

Visualization

Interactive Views

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
		FE2	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		SUC	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]

	Sites
		AC1	[ RasMol ]	+environment [ RasMol ]
		AC2	[ RasMol ]	+environment [ RasMol ]
		AC3	[ RasMol ]	+environment [ RasMol ]
		AC4	[ RasMol ]	+environment [ RasMol ]

	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 3vf1)

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

Still Images

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)

Databases and Analysis Tools

Databases

Access by PDB/NDB ID
	3vf1
		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
	Q2N410_9CNID \| Q2N410
		Comparative Protein Structure Models	:	ModBase
		Genomic Information	:	Ensembl
		Protein-protein Interaction	:	DIP
		Sequence, Family and Domain Information	:	InterPro \| Pfam \| SMART \| UniProtKB/TrEMBL

Access by Enzyme Classificator (EC Number)
	(no 'Enzyme Classificator' available)
		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

Analysis Tools

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
	Q2N410_9CNID \| Q2N410
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

Description