3NMP - 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)

Title :   CRYSTAL STRUCTURE OF THE ABSCISIC RECEPTOR PYL2 MUTANT A93F IN COMPLEX WITH PYRABACTIN

Authors :   X. E. Zhou, K. Melcher, L. -M. Ng, F. -F. Soon, Y. Xu, K. M. Suino-Powell, A J. Li, E. -L. Yong, H. E. Xu

Date :   22 Jun 10 (Deposition) - 25 Aug 10 (Release) - 15 Sep 10 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.10

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

Keywords :   Pyl2, Pyrabactin, Plant Hormone Receptor, Helix-Grip Fold, Hormone Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   K. Melcher, Y. Xu, L. M. Ng, X. E. Zhou, F. F. Soon, V. Chinnusamy, K. M. Suino-Powell, A. Kovach, F. S. Tham, S. R. Cutler, J. Li, E. L. Yong J. K. Zhu, H. E. Xu
Identification And Mechanism Of Aba Receptor Antagonism.
Nat. Struct. Mol. Biol. V. 17 1102 2010
PubMed-ID: 20729862 | Reference-DOI: 10.1038/NSMB.1887

Molecule 1 - ABSCISIC ACID RECEPTOR PYL2
	Chains	:	A, B, C
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET24A
	Expression System Strain	:	BL21
	Expression System Taxid	:	562
	Expression System Vector	:	PLASMID
	Gene	:	PYL2, RCAR14, AT2G26040, T19L18.15
	Mutation	:	YES
	Organism Common	:	MOUSE-EAR CRESS,THALE-CRESS
	Organism Scientific	:	ARABIDOPSIS THALIANA
	Organism Taxid	:	3702
	Synonym	:	PYR1-LIKE PROTEIN 2, REGULATORY COMPONENTS OF ABA RECEPTOR 14

		1	2	3
Asymmetric Unit	:	A	B	C
Biological Unit 1 (1x)	:	A	B
Biological Unit 2 (2x)	:			C

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 3)

No.	Name	Count	Type	Full Name
1	PYV	3	Ligand/Ion	4-BROMO-N-(PYRIDIN-2-YLMETHYL)NAPHTHALENE-1-SULFONAMIDE

Biological Unit 1 (1, 2)

No.	Name	Count	Type	Full Name
1	PYV	2	Ligand/Ion	4-BROMO-N-(PYRIDIN-2-YLMETHYL)NAPHTHALENE-1-SULFONAMIDE

Biological Unit 2 (1, 2)

No.	Name	Count	Type	Full Name
1	PYV	2	Ligand/Ion	4-BROMO-N-(PYRIDIN-2-YLMETHYL)NAPHTHALENE-1-SULFONAMIDE

Asymmetric Unit (3, 3)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	LYS A:64 , VAL A:87 , GLU A:98 , PHE A:112 , VAL A:114 , LEU A:121 , TYR A:124 , VAL A:169 , HOH A:215	BINDING SITE FOR RESIDUE PYV A 900
2	AC2	SOFTWARE	LYS B:64 , HIS B:65 , GLU B:98 , PHE B:112 , TYR B:124 , VAL B:169 , ASN B:173 , HOH B:280	BINDING SITE FOR RESIDUE PYV B 900
3	AC3	SOFTWARE	LYS C:64 , VAL C:85 , GLU C:98 , VAL C:114 , LEU C:121 , TYR C:124 , VAL C:169 , ASN C:173 , HOH C:245	BINDING SITE FOR RESIDUE PYV C 900

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

(no "Cis Peptide Bond" information available for 3NMP)

(no "SAP(SNP)/Variant" information available for 3NMP)

(no "PROSITE Motif" information available for 3NMP)

(no "Exon" information available for 3NMP)

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:176
 aligned with PYL2_ARATH | O80992 from UniProtKB/Swiss-Prot  Length:190

    Alignment length:176
                                    22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182      
           PYL2_ARATH    13 EEQKTLEPVIKTYHQFEPDPTTCTSLITQRIHAPASVVWPLIRRFDNPERYKHFVKRCRLISGDGDVGSVREVTVISGLPASTSTERLEFVDDDHRVLSFRVVGGEHRLKNYKSVTSVNEFLNQDSGKVYTVVLESYTVDIPEGNTEEDTKMFVDTVVKLNLQKLGVAATSAPMHD 188
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhh.......eeeeeeeeee..hhhhhhhhhhh..hhhhh...eeeeeeee.......eeeeee......eeeeeeeeeee....eeeeee..........eeeeeeeeee......eeeeeeeeeeee.....hhhhhhhhhhhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3nmp A  13 SEQKTLEPVIKTYHQFEPDPTTCTSLITQRIHAPASVVWPLIRRFDNPERYKHFVKRCRLISGDGDVGSVREVTVISGLPFSTSTERLEFVDDDHRVLSFRVVGGEHRLKNYKSVTSVNEFLNQDSGKVYTVVLESYTVDIPEGNTEEDTKMFVDTVVKLNLQKLGVAATSAPMHD 188
                                    22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182

Chain B from PDB  Type:PROTEIN  Length:176
 aligned with PYL2_ARATH | O80992 from UniProtKB/Swiss-Prot  Length:190

    Alignment length:176
                                    22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182      
           PYL2_ARATH    13 EEQKTLEPVIKTYHQFEPDPTTCTSLITQRIHAPASVVWPLIRRFDNPERYKHFVKRCRLISGDGDVGSVREVTVISGLPASTSTERLEFVDDDHRVLSFRVVGGEHRLKNYKSVTSVNEFLNQDSGKVYTVVLESYTVDIPEGNTEEDTKMFVDTVVKLNLQKLGVAATSAPMHD 188
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhh.......eeeeeeeeee..hhhhhhhhhhh..hhhhh...eeeeeeee.......eeeeee......eeeeeeeeeee....eeeeee..........eeeeeeeeee......eeeeeeeeeeee.....hhhhhhhhhhhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3nmp B  13 SEQKTLEPVIKTYHQFEPDPTTCTSLITQRIHAPASVVWPLIRRFDNPERYKHFVKRCRLISGDGDVGSVREVTVISGLPFSTSTERLEFVDDDHRVLSFRVVGGEHRLKNYKSVTSVNEFLNQDSGKVYTVVLESYTVDIPEGNTEEDTKMFVDTVVKLNLQKLGVAATSAPMHD 188
                                    22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182

Chain C from PDB  Type:PROTEIN  Length:176
 aligned with PYL2_ARATH | O80992 from UniProtKB/Swiss-Prot  Length:190

    Alignment length:176
                                    22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182      
           PYL2_ARATH    13 EEQKTLEPVIKTYHQFEPDPTTCTSLITQRIHAPASVVWPLIRRFDNPERYKHFVKRCRLISGDGDVGSVREVTVISGLPASTSTERLEFVDDDHRVLSFRVVGGEHRLKNYKSVTSVNEFLNQDSGKVYTVVLESYTVDIPEGNTEEDTKMFVDTVVKLNLQKLGVAATSAPMHD 188
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) ---------------------Polyketide_cyc2-3nmpC01 C:34-181                                                                                                                    ------- Pfam domains (1)
           Pfam domains (2) ---------------------Polyketide_cyc2-3nmpC02 C:34-181                                                                                                                    ------- Pfam domains (2)
           Pfam domains (3) ---------------------Polyketide_cyc2-3nmpC03 C:34-181                                                                                                                    ------- Pfam domains (3)
         Sec.struct. author hhhhhhhhhhhhhh.......eeeeeeeeee..hhhhhhhhhhh..hhhhh...eeeeeeee.......eeeeee......eeeeeeeeeee....eeeeeeee.....eeeeeeeeeeeee......eeeeeeeeeeee.....hhhhhhhhhhhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3nmp C  13 SEQKTLEPVIKTYHQFEPDPTTCTSLITQRIHAPASVVWPLIRRFDNPERYKHFVKRCRLISGDGDVGSVREVTVISGLPFSTSTERLEFVDDDHRVLSFRVVGGEHRLKNYKSVTSVNEFLNQDSGKVYTVVLESYTVDIPEGNTEEDTKMFVDTVVKLNLQKLGVAATSAPMHD 188
                                    22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182

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 '\|'

(no "SCOP Domain" information available for 3NMP)

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

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: Bet_V_1_like (93)

Family: Polyketide_cyc2 (26)

Arabidopsis thaliana (Mouse-ear cress) (24)

1a	Polyketide_cyc2-3nmpC01	C:34-181
1b	Polyketide_cyc2-3nmpC02	C:34-181
1c	Polyketide_cyc2-3nmpC03	C:34-181

Asymmetric Unit(hide GO term definitions)

Chain A,B,C (PYL2_ARATH | O80992)

molecular function
	GO:0010427	abscisic acid binding	Interacting selectively and non-covalently with abscisic acid, plant hormones that regulate aspects of plant growth.
	GO:0005515	protein binding	Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
	GO:0042803	protein homodimerization activity	Interacting selectively and non-covalently with an identical protein to form a homodimer.
	GO:0004864	protein phosphatase inhibitor activity	Stops, prevents or reduces the activity of a protein phosphatase, an enzyme that hydrolyzes phosphate groups from phosphorylated proteins.
	GO:0004872	receptor activity	Combining with an extracellular or intracellular messenger to initiate a change in cell activity.
biological process
	GO:0009738	abscisic acid-activated signaling pathway	A series of molecular signals generated by the binding of the plant hormone abscisic acid (ABA) to a receptor, and ending with modulation of a cellular process, e.g. transcription.
	GO:0043086	negative regulation of catalytic activity	Any process that stops or reduces the activity of an enzyme.
	GO:0080163	regulation of protein serine/threonine phosphatase activity	Any process that modulates the frequency, rate or extent of protein serine/threonine phosphatase activity: catalysis of the reaction: protein serine/threonine phosphate + H2O = protein serine/threonine + phosphate.
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	GO:0016020	membrane	A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
	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.
	GO:0005886	plasma membrane	The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.

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
		PYV	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]

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

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

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
	3nmp
		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
	PYL2_ARATH \| O80992
		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)
	(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

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
	PYL2_ARATH \| O80992
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

3kaz	APO PYL2
3kb0	PYL2 IN COMPLEX WITH ABSCISIC ACID
3mnh	WILD TYPE PYL2 IN COMPLEX WITH PYRABACTIN
3nmn
3nmt
3nmv

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (1, 3)

Sites (3, 3)

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

Classification and Annotation

SCOP Domains (0, 0)

CATH Domains (0, 0)

Pfam Domains (1, 3)

Gene Ontology (12, 12)

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