4D28 - JenaLib

Asymmetric Unit (Jmol Viewer)

Biological Unit 1 (Jmol Viewer)

Biological Unit 2 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF THE KINASE DOMAIN OF SNRK3.11 AT5G35410

Authors :   J. M. Gonzalez-Rubio, A. Chaves-Sanjuan, M. J. Sanchez-Barrena, A. Al

Date :   08 May 14 (Deposition) - 15 Oct 14 (Release) - 17 Dec 14 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   3.30

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

Keywords :   Transferase, Salt Stress, Sodium Transport, Ion Homeostasis (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   A. Chaves-Sanjuan, M. J. Sanchez-Barrena, J. M. Gonzalez-Rubio, M. Moreno, P. Ragel, M. Jimenez, J. M. Pardo, M. Martinez-Ripoll, F. J. Quintero, A. Albert
Structural Basis Of The Regulatory Mechanism Of The Plant Cipk Family Of Protein Kinases Controlling Ion Homeostasis And Abiotic Stress
Proc. Natl. Acad. Sci. Usa V. 111 E4532 2014
PubMed-ID: 25288725 | Reference-DOI: 10.1073/PNAS.1407610111

Molecule 1 - CBL-INTERACTING SERINE/THREONINE-PROTEIN KINASE 24
	Chains	:	A, B, C, D
	EC Number	:	2.7.11.1
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PGEX4T2
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Variant	:	ROSETTA 2 PLYSS
	Expression System Vector Type	:	PLASMID
	Mutation	:	YES
	Organism Common	:	THALE CRESS
	Organism Scientific	:	ARABIDOPSIS THALIANA
	Organism Taxid	:	3702
	Synonym	:	PROTEIN SALT OVERLY SENSITIVE 2, SNF1-RELATED KINASE 3.11, SNRK3.11 AT5G35410

		1	2	3	4
Asymmetric Unit	:	A	B	C	D
Biological Unit 1 (1x)	:	A			D
Biological Unit 2 (1x)	:		B	C

Summary Information (see also Sequences/Alignments below)

(no "Ligand,Modified Residues,Ions" information available for 4D28)

(no "Site" information available for 4D28)

(no "SS Bond" information available for 4D28)

Asymmetric Unit

No.	Residues
1	Arg A:15	-	Thr A:16
2	Glu A:161	-	Gly A:162
3	Arg B:15	-	Thr B:16
4	Arg C:15	-	Thr C:16
5	Arg D:15	-	Thr D:16
6	Gly D:171	-	Thr D:172

(no "SAP(SNP)/Variant" information available for 4D28)

Asymmetric Unit (2, 8)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	PROTEIN_KINASE_ATP	PS00107	Protein kinases ATP-binding region signature.	CIPKO_ARATH	17-49	4	A:17-49 B:17-49 C:17-49 D:21-49
2	PROTEIN_KINASE_ST	PS00108	Serine/Threonine protein kinases active-site signature.	CIPKO_ARATH	130-142	4	A:130-142 B:130-142 C:130-142 D:130-142

Biological Unit 1 (2, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	PROTEIN_KINASE_ATP	PS00107	Protein kinases ATP-binding region signature.	CIPKO_ARATH	17-49	2	A:17-49 - - D:21-49
2	PROTEIN_KINASE_ST	PS00108	Serine/Threonine protein kinases active-site signature.	CIPKO_ARATH	130-142	2	A:130-142 - - D:130-142

Biological Unit 2 (2, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	PROTEIN_KINASE_ATP	PS00107	Protein kinases ATP-binding region signature.	CIPKO_ARATH	17-49	2	- B:17-49 C:17-49 -
2	PROTEIN_KINASE_ST	PS00108	Serine/Threonine protein kinases active-site signature.	CIPKO_ARATH	130-142	2	- B:130-142 C:130-142 -

(no "Exon" information available for 4D28)

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:274
 aligned with CIPKO_ARATH | Q9LDI3 from UniProtKB/Swiss-Prot  Length:446

    Alignment length:282
                                    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  
          CIPKO_ARATH     8 VGKYEVGRTIGEGTFAKVKFARNTDTGDNVAIKIMAKSTILKNRMVDQIKREISIMKIVRHPNIVRLYEVLASPSKIYIVLEFVTGGELFDRIVHKGRLEESESRKYFQQLVDAVAHCHCKGVYHRDLKPENLLLDTNGNLKVSDFGLSALPQEGVELLRTTCGTPNYVAPEVLSGQGYDGSAADIWSCGVILFVILAGYLPFSETDLPGLYRKINAAEFSCPPWFSAEVKFLIHRILDPNPKTRIQIQGIKKDPWFRLNYVPIRAREEEEVNLDDIRAVFD 289
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...eee....-----.eeeeeee....eeeeeeeeehhhhhh..hhhhhhhhhhhhhhh..........eee...eeeeee.....eehhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhh...........eee.....eee............---...........hhhhhhh...hhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhh........hhhhhhhhhhhh........hhhhhhhhhhhhh.............hhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ---------PROTEIN_KINASE_ATP  PDB: A:17-49 --------------------------------------------------------------------------------PROTEIN_KINAS--------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4d28 A   8 VGKYEVGRTI-----AKVKFARNTDTGDNVAIKIMAKSTILKNRMVDQIKREISIMKIVRHPNIVRLYEVLASKSKIYIVLEFVTGGELFDRIVHKGRLKEDESRKYFQQLVDAVAHCHSKGVYHRDLKPENLLLDTNGNLKVSDFGLSALPQEG---LNDTCGTPNYVAPEVLSGQGYDGSAADIWSCGVILFVILAGYLPFSETDLPGLYRKINAAEFDCPPWFSAEVKFLIHRILDPNPKTRIQIQGIKKDPWFRKNYVPIRAREEEEVNLDDIRAVFD 289
                                    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  
                                    17    23                                                                                                                                        162 166

Chain B from PDB  Type:PROTEIN  Length:277
 aligned with CIPKO_ARATH | Q9LDI3 from UniProtKB/Swiss-Prot  Length:446

    Alignment length:283
                                    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   
          CIPKO_ARATH     7 RVGKYEVGRTIGEGTFAKVKFARNTDTGDNVAIKIMAKSTILKNRMVDQIKREISIMKIVRHPNIVRLYEVLASPSKIYIVLEFVTGGELFDRIVHKGRLEESESRKYFQQLVDAVAHCHCKGVYHRDLKPENLLLDTNGNLKVSDFGLSALPQEGVELLRTTCGTPNYVAPEVLSGQGYDGSAADIWSCGVILFVILAGYLPFSETDLPGLYRKINAAEFSCPPWFSAEVKFLIHRILDPNPKTRIQIQGIKKDPWFRLNYVPIRAREEEEVNLDDIRAVFD 289
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eee..........eeeeeee.....eeeeeeeehhhhhh..hhhhhhhhhhhhhhh.......eeeeee...eeeeeee......hhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhh......hhh.eee.....eee..........------..........hhhhhh....hhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhh........hhhhhhhhhhhh........hhhhhhhhhhhhh.............hhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------PROTEIN_KINASE_ATP  PDB: B:17-49 --------------------------------------------------------------------------------PROTEIN_KINAS--------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4d28 B   7 RVGKYEVGRTIGEGTFAKVKFARNTDTGDNVAIKIMAKSTILKNRMVDQIKREISIMKIVRHPNIVRLYEVLASKSKIYIVLEFVTGGELFDRIVHKGRLKEDESRKYFQQLVDAVAHCHSKGVYHRDLKPENLLLDTNGNLKVSDFGLSALPQ------NDTCGTPNYVAPEVLSGQGYDGSAADIWSCGVILFVILAGYLPFSETDLPGLYRKINAAEFDCPPWFSAEVKFLIHRILDPNPKTRIQIQGIKKDPWFRKNYVPIRAREEEEVNLDDIRAVFD 289
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156   |     -|      176       186       196       206       216       226       236       246       256       266       276       286   
                                                                                                                                                                                   160    167

Chain C from PDB  Type:PROTEIN  Length:279
 aligned with CIPKO_ARATH | Q9LDI3 from UniProtKB/Swiss-Prot  Length:446

    Alignment length:283
                                    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   
          CIPKO_ARATH     7 RVGKYEVGRTIGEGTFAKVKFARNTDTGDNVAIKIMAKSTILKNRMVDQIKREISIMKIVRHPNIVRLYEVLASPSKIYIVLEFVTGGELFDRIVHKGRLEESESRKYFQQLVDAVAHCHCKGVYHRDLKPENLLLDTNGNLKVSDFGLSALPQEGVELLRTTCGTPNYVAPEVLSGQGYDGSAADIWSCGVILFVILAGYLPFSETDLPGLYRKINAAEFSCPPWFSAEVKFLIHRILDPNPKTRIQIQGIKKDPWFRLNYVPIRAREEEEVNLDDIRAVFD 289
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....ee..........eeeeee......eeeeeeeehhhhhh..hhhhhhhhhhhhhhh.......eeeeee...eeeeeee.....hhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhh.......hhh.eee.....eee...........----...........hhhhhhh...hhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhh........hhhhhhhhhhhh........hhhhhhhhhhhhh.............hhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------PROTEIN_KINASE_ATP  PDB: C:17-49 --------------------------------------------------------------------------------PROTEIN_KINAS--------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4d28 C   7 RVGKYEVGRTIGEGTFAKVKFARNTDTGDNVAIKIMAKSTILKNRMVDQIKREISIMKIVRHPNIVRLYEVLASKSKIYIVLEFVTGGELFDRIVHKGRLKEDESRKYFQQLVDAVAHCHSKGVYHRDLKPENLLLDTNGNLKVSDFGLSALPQE----LNDTCGTPNYVAPEVLSGQGYDGSAADIWSCGVILFVILAGYLPFSETDLPGLYRKINAAEFDCPPWFSAEVKFLIHRILDPNPKTRIQIQGIKKDPWFRKNYVPIRAREEEEVNLDDIRAVFD 289
                                    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   
                                                                                                                                                                                    161  166

Chain D from PDB  Type:PROTEIN  Length:271
 aligned with CIPKO_ARATH | Q9LDI3 from UniProtKB/Swiss-Prot  Length:446

    Alignment length:280
                                    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
          CIPKO_ARATH    10 KYEVGRTIGEGTFAKVKFARNTDTGDNVAIKIMAKSTILKNRMVDQIKREISIMKIVRHPNIVRLYEVLASPSKIYIVLEFVTGGELFDRIVHKGRLEESESRKYFQQLVDAVAHCHCKGVYHRDLKPENLLLDTNGNLKVSDFGLSALPQEGVELLRTTCGTPNYVAPEVLSGQGYDGSAADIWSCGVILFVILAGYLPFSETDLPGLYRKINAAEFSCPPWFSAEVKFLIHRILDPNPKTRIQIQGIKKDPWFRLNYVPIRAREEEEVNLDDIRAVFD 289
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..ee...----...eee.ee.hhhh....eeeeehhhhhh..hhhhhhhhhhhhhh........eeeeee...eeeeee......hhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhh...........eee.....eee..........-----...........hhhhhhh...hhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhh........hhhhhhhhhhhh........hhhhhhhhhhhhh.............hhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------PROTEIN_KINASE_ATP  PDB: D:21-49 --------------------------------------------------------------------------------PROTEIN_KINAS--------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4d28 D  10 KYEVGRT----TFAKVKFARNTDTGDNVAIKIMAKSTILKNRMVDQIKREISIMKIVRHPNIVRLYEVLASKSKIYIVLEFVTGGELFDRIVHKGRLKEDESRKYFQQLVDAVAHCHSKGVYHRDLKPENLLLDTNGNLKVSDFGLSALPQ-----LNDTCGTPNYVAPEVLSGQGYDGSAADIWSCGVILFVILAGYLPFSETDLPGLYRKINAAEFDCPPWFSAEVKFLIHRILDPNPKTRIQIQGIKKDPWFRKNYVPIRAREEEEVNLDDIRAVFD 289
                                  |  - |      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
                                 16   21                                                                                                                                        160   166

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 4D28)

(no "CATH Domain" information available for 4D28)

(no "Pfam Domain" information available for 4D28)

Asymmetric Unit(hide GO term definitions)

Chain A,B,C,D (CIPKO_ARATH | Q9LDI3)

molecular function
	GO:0005524	ATP binding	Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
	GO:0016301	kinase activity	Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule.
	GO:0000166	nucleotide binding	Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
	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:0004672	protein kinase activity	Catalysis of the phosphorylation of an amino acid residue in a protein, usually according to the reaction: a protein + ATP = a phosphoprotein + ADP.
	GO:0004674	protein serine/threonine kinase activity	Catalysis of the reactions: ATP + protein serine = ADP + protein serine phosphate, and ATP + protein threonine = ADP + protein threonine phosphate.
	GO:0016740	transferase activity	Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
biological process
	GO:0035556	intracellular signal transduction	The process in which a signal is passed on to downstream components within the cell, which become activated themselves to further propagate the signal and finally trigger a change in the function or state of the cell.
	GO:0016310	phosphorylation	The process of introducing a phosphate group into a molecule, usually with the formation of a phosphoric ester, a phosphoric anhydride or a phosphoric amide.
	GO:0006468	protein phosphorylation	The process of introducing a phosphate group on to a protein.
	GO:0009651	response to salt 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 a stimulus indicating an increase or decrease in the concentration of salt (particularly but not exclusively sodium and chloride ions) in the environment.
	GO:0007165	signal transduction	The cellular process in which a signal is conveyed to trigger a change in the activity or state of a cell. Signal transduction begins with reception of a signal (e.g. a ligand binding to a receptor or receptor activation by a stimulus such as light), or for signal transduction in the absence of ligand, signal-withdrawal or the activity of a constitutively active receptor. Signal transduction ends with regulation of a downstream cellular process, e.g. regulation of transcription or regulation of a metabolic process. Signal transduction covers signaling from receptors located on the surface of the cell and signaling via molecules located within the cell. For signaling between cells, signal transduction is restricted to events at and within the receiving cell.
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	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:0009705	plant-type vacuole membrane	The lipid bilayer surrounding a vacuole that retains the same shape regardless of cell cycle phase. The membrane separates its contents from the cytoplasm of the cell. An example of this component is found in Arabidopsis thaliana.

Asymmetric Unit
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	Ligands, Modified Residues, Ions
(no "Ligands, Modified Residues, Ions" information available for 4d28)

	Sites
(no "Sites" information available for 4d28)

	Cis Peptide Bonds
		Arg A:15 - Thr A:16	[ RasMol ]
		Arg B:15 - Thr B:16	[ RasMol ]
		Arg C:15 - Thr C:16	[ RasMol ]
		Arg D:15 - Thr D:16	[ RasMol ]
		Glu A:161 - Gly A:162	[ RasMol ]
		Gly D:171 - Thr D:172	[ RasMol ]

Biological Units
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		Biological Unit 2	[ Jena3D ]

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	4d28
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	2.7.11.1
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	CIPKO_ARATH \| Q9LDI3	:	2ehb

4czt	CRYSTAL STRUCTURE OF THE KINASE DOMAIN OF SNRK3.23 AT1G30270
4czu	CRYSTAL STRUCTURE OF THE KINASE DOMAIN OF SNRK3.23 AT1G30270 T190D MUTANT

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (0, 0)

Sites (0, 0)

SS Bonds (0, 0)

Cis Peptide Bonds (6, 6)

Sequence-Structure Mapping

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