2R5T - 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)

Biological Unit 3 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF INACTIVE SERUM AND GLUCOCORTICOID-REGULATED KINASE 1 IN COMPLEX WITH AMP-PNP

Authors :   B. Zhao, R. Lehr, A. M. Smallwood, T. F. Ho, K. Maley, T. Randall, M. S. Head, K. K. Koretke, C. G. Schnackenberg

Date :   04 Sep 07 (Deposition) - 09 Sep 08 (Release) - 20 Jan 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.90

Chains :   Asym. Unit : A
Biol. Unit 1: A  (1x)
Biol. Unit 2: A  (2x)
Biol. Unit 3: A  (2x)

Keywords :   Agc Protein Kinase, Apoptosis, Atp-Binding, Cytoplasm, Endoplasmic Reticulum, Nucleotide-Binding, Nucleus, Phosphorylation, Serine/Threonine-Protein Kinase, Transferase, Ubl Conjugation (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   B. Zhao, R. Lehr, A. M. Smallwood, T. F. Ho, K. Maley, T. Randall, M. S. Head, K. K. Koretke, C. G. Schnackenberg
Crystal Structure Of The Kinase Domain Of Serum And Glucocorticoid-Regulated Kinase 1 In Complex With Amp Pnp.
Protein Sci. V. 16 2761 2007
PubMed-ID: 17965184 | Reference-DOI: 10.1110/PS.073161707
(for further references see the PDB file header)

Molecule 1 - SERINE/THREONINE-PROTEIN KINASE SGK1
	Chains	:	A
	EC Number	:	2.7.11.1
	Engineered	:	YES
	Expression System	:	BACULOVIRUS
	Expression System Vector Type	:	GATWAY GST TAGGED EXPRESSION VECTOR
	Gene	:	SGK, SGK1
	Mutation	:	YES
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Synonym	:	SERUM/GLUCOCORTICOID-REGULATED KINASE 1

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (3, 3)

No.	Name	Count	Type	Full Name
1	ANP	1	Ligand/Ion	PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
2	MG	1	Ligand/Ion	MAGNESIUM ION
3	SO4	1	Ligand/Ion	SULFATE ION

Biological Unit 1 (2, 2)

No.	Name	Count	Type	Full Name
1	ANP	1	Ligand/Ion	PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
2	MG	-1	Ligand/Ion	MAGNESIUM ION
3	SO4	1	Ligand/Ion	SULFATE ION

Biological Unit 2 (2, 4)

No.	Name	Count	Type	Full Name
1	ANP	2	Ligand/Ion	PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
2	MG	-1	Ligand/Ion	MAGNESIUM ION
3	SO4	2	Ligand/Ion	SULFATE ION

Biological Unit 3 (2, 4)

No.	Name	Count	Type	Full Name
1	ANP	2	Ligand/Ion	PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
2	MG	-1	Ligand/Ion	MAGNESIUM ION
3	SO4	2	Ligand/Ion	SULFATE ION

Asymmetric Unit (3, 3)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	GLU A:226	BINDING SITE FOR RESIDUE MG A 600
2	AC2	SOFTWARE	SER A:255 , THR A:256 , HOH A:737 , HOH A:778	BINDING SITE FOR RESIDUE SO4 A 700
3	AC3	SOFTWARE	ILE A:104 , GLY A:107 , SER A:108 , PHE A:109 , ALA A:125 , LYS A:127 , ASP A:177 , ILE A:179 , ARG A:190 , LYS A:224 , GLU A:226 , ASN A:227 , LEU A:229 , THR A:239 , HOH A:789 , HOH A:795 , HOH A:873 , HOH A:907	BINDING SITE FOR RESIDUE ANP A 500

(no "SS Bond" information available for 2R5T)

(no "Cis Peptide Bond" information available for 2R5T)

Asymmetric Unit (2, 2)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_041071	V	219	I	SGK1_HUMAN	Polymorphism	34133418	A	V	219	I
2	UniProt	VAR_041072	A	342	V	SGK1_HUMAN	Polymorphism	55932330	A	A	342	V

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

Biological Unit 1 (2, 2)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_041071	V	219	I	SGK1_HUMAN	Polymorphism	34133418	A	V	219	I
2	UniProt	VAR_041072	A	342	V	SGK1_HUMAN	Polymorphism	55932330	A	A	342	V

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

Biological Unit 2 (2, 4)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_041071	V	219	I	SGK1_HUMAN	Polymorphism	34133418	A	V	219	I
2	UniProt	VAR_041072	A	342	V	SGK1_HUMAN	Polymorphism	55932330	A	A	342	V

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

Biological Unit 3 (2, 4)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_041071	V	219	I	SGK1_HUMAN	Polymorphism	34133418	A	V	219	I
2	UniProt	VAR_041072	A	342	V	SGK1_HUMAN	Polymorphism	55932330	A	A	342	V

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

Asymmetric Unit (3, 3)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	PROTEIN_KINASE_ATP	PS00107	Protein kinases ATP-binding region signature.	SGK1_HUMAN	104-136	1	A:104-135
2	PROTEIN_KINASE_ST	PS00108	Serine/Threonine protein kinases active-site signature.	SGK1_HUMAN	218-230	1	A:218-230
3	AGC_KINASE_CTER	PS51285	AGC-kinase C-terminal domain profile.	SGK1_HUMAN	356-431	1	A:356-378

Biological Unit 1 (3, 3)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	PROTEIN_KINASE_ATP	PS00107	Protein kinases ATP-binding region signature.	SGK1_HUMAN	104-136	1	A:104-135
2	PROTEIN_KINASE_ST	PS00108	Serine/Threonine protein kinases active-site signature.	SGK1_HUMAN	218-230	1	A:218-230
3	AGC_KINASE_CTER	PS51285	AGC-kinase C-terminal domain profile.	SGK1_HUMAN	356-431	1	A:356-378

Biological Unit 2 (3, 6)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	PROTEIN_KINASE_ATP	PS00107	Protein kinases ATP-binding region signature.	SGK1_HUMAN	104-136	2	A:104-135
2	PROTEIN_KINASE_ST	PS00108	Serine/Threonine protein kinases active-site signature.	SGK1_HUMAN	218-230	2	A:218-230
3	AGC_KINASE_CTER	PS51285	AGC-kinase C-terminal domain profile.	SGK1_HUMAN	356-431	2	A:356-378

Biological Unit 3 (3, 6)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	PROTEIN_KINASE_ATP	PS00107	Protein kinases ATP-binding region signature.	SGK1_HUMAN	104-136	2	A:104-135
2	PROTEIN_KINASE_ST	PS00108	Serine/Threonine protein kinases active-site signature.	SGK1_HUMAN	218-230	2	A:218-230
3	AGC_KINASE_CTER	PS51285	AGC-kinase C-terminal domain profile.	SGK1_HUMAN	356-431	2	A:356-378

(no "Exon" information available for 2R5T)

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
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Chain A from PDB  Type:PROTEIN  Length:284
 aligned with SGK1_HUMAN | O00141 from UniProtKB/Swiss-Prot  Length:431

    Alignment length:297
                                    91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       
           SGK1_HUMAN    82 QINLGPSSNPHAKPSDFHFLKVIGKGSFGKVLLARHKAEEVFYAVKVLQKKAILKKKEEKHIMSERNVLLKNVKHPFLVGLHFSFQTADKLYFVLDYINGGELFYHLQRERCFLEPRARFYAAEIASALGYLHSLNIVYRDLKPENILLDSQGHIVLTDFGLCKENIEHNSTTSTFCGTPEYLAPEVLHKQPYDRTVDWWCLGAVLYEMLYGLPPFYSRNTAEMYDNILNKPLQLKPNITNSARHLLEGLLQKDRTKRLGAKDDFMEIKSHVFFSLINWDDLINKKITPPFNPNVSG 378
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------2r5tA01 A:88-182 Phosphorylase Kinase; domain 1                                                2r5tA02 A:183-372 Transferase(Phosphotransferase) domain 1                                                                                                                                    ------ CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ............hhh.eeeeeeee.....eeeeeee.....eeeeeeee.hhh.-------------.............eeeeee...eeeeeee.....hhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhh.......hhh.eee.....eee.....hhhhh................hhhhhh.....hhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhh........hhhhhhhhhhhh..hhhhh.....hhhhhhhhhhhh..hhhhhhh............. Sec.struct. author
                 SAPs(SNPs) -----------------------------------------------------------------------------------------------------------------------------------------I--------------------------------------------------------------------------------------------------------------------------V------------------------------------ SAPs(SNPs)
                    PROSITE ----------------------PROTEIN_KINASE_ATP  PDB: A:104-13---------------------------------------------------------------------------------PROTEIN_KINAS-----------------------------------------------------------------------------------------------------------------------------AGC_KINASE_CTER         PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2r5t A  82 QINLGPSSNPHAKPSDFHFLKVIGKGSFGKVLLARHKAEEVFYAVKVLQKKAIL-------------VLLKNVKHPFLVGLHFSFQTADKLYFVLDYINGGELFYHLQRERCFLEPRARFYAAEIASALGYLHSLNIVYRDLKPENILLDSQGHIVLTDFGLCKENIEHNSTTSTFCGTPEYLAPEVLHKQPYDRTVDWWCLGAVLYEMLYGLPPFYSRNTAEMYDNILNKPLQLKPNITNSARHLLEGLLQKDRTKRLGAKDDFMEIKSHVFFSLINWDDLINKKITPPFNPNVSG 378
                                    91       101       111       121       131   |     -       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       
                                                                               135           149

Legend:		→ Mismatch	(orange background)
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	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 2R5T)

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: 2-Layer Sandwich (8480)

Topology: Phosphorylase Kinase; domain 1 (1392)

Homologous Superfamily: Phosphorylase Kinase; domain 1 (1392)

Human (Homo sapiens) (1036)

2r5tA01

A:88-182

Class: Mainly Alpha (13335)

Architecture: Orthogonal Bundle (10391)

Topology: Transferase(Phosphotransferase); domain 1 (1379)

Homologous Superfamily: Transferase(Phosphotransferase) domain 1 (1379)

Human (Homo sapiens) (1049)

2r5tA02

A:183-372

(no "Pfam Domain" information available for 2R5T)

Asymmetric Unit(hide GO term definitions)

Chain A (SGK1_HUMAN | O00141)

molecular function
	GO:0043423	3-phosphoinositide-dependent protein kinase binding	Interacting selectively and non-covalently with a 3-phosphoinositide-dependent protein kinase.
	GO:0005524	ATP binding	Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
	GO:0005246	calcium channel regulator activity	Modulates the activity of a calcium channel.
	GO:0017081	chloride channel regulator activity	Modulates the activity of a chloride channel.
	GO:0048037	cofactor binding	Interacting selectively and non-covalently with a cofactor, a substance that is required for the activity of an enzyme or other protein. Cofactors may be inorganic, such as the metal atoms zinc, iron, and copper in certain forms, or organic, in which case they are referred to as coenzymes. Cofactors may either be bound tightly to active sites or bind loosely with the substrate.
	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:0015459	potassium channel regulator activity	Modulates potassium channel activity via direct interaction interaction with a potassium channel (binding or modification).
	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:0004712	protein serine/threonine/tyrosine kinase activity	Catalysis of the reactions: ATP + a protein serine = ADP + protein serine phosphate; ATP + a protein threonine = ADP + protein threonine phosphate; and ATP + a protein tyrosine = ADP + protein tyrosine phosphate.
	GO:0017080	sodium channel regulator activity	Modulates the activity of a sodium channel.
	GO:0048156	tau protein binding	Interacting selectively and non-covalently with tau protein. tau is a microtubule-associated protein, implicated in Alzheimer's disease, Down Syndrome and ALS.
	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:0006915	apoptotic process	A programmed cell death process which begins when a cell receives an internal (e.g. DNA damage) or external signal (e.g. an extracellular death ligand), and proceeds through a series of biochemical events (signaling pathway phase) which trigger an execution phase. The execution phase is the last step of an apoptotic process, and is typically characterized by rounding-up of the cell, retraction of pseudopodes, reduction of cellular volume (pyknosis), chromatin condensation, nuclear fragmentation (karyorrhexis), plasma membrane blebbing and fragmentation of the cell into apoptotic bodies. When the execution phase is completed, the cell has died.
	GO:0006974	cellular response to DNA damage stimulus	Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus indicating damage to its DNA from environmental insults or errors during metabolism.
	GO:0006883	cellular sodium ion homeostasis	Any process involved in the maintenance of an internal steady state of sodium ions at the level of a cell.
	GO:0043402	glucocorticoid mediated signaling pathway	A series of molecular signals mediated by the detection of a glucocorticoid hormone.
	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:0034220	ion transmembrane transport	A process in which an ion is transported from one side of a membrane to the other by means of some agent such as a transporter or pore.
	GO:0007616	long-term memory	The memory process that deals with the storage, retrieval and modification of information a long time (typically weeks, months or years) after receiving that information. This type of memory is typically dependent on gene transcription regulated by second messenger activation.
	GO:0007019	microtubule depolymerization	The removal of tubulin heterodimers from one or both ends of a microtubule.
	GO:0043066	negative regulation of apoptotic process	Any process that stops, prevents, or reduces the frequency, rate or extent of cell death by apoptotic process.
	GO:0031115	negative regulation of microtubule polymerization	Any process that stops, prevents, or reduces the frequency, rate or extent of microtubule polymerization.
	GO:0048812	neuron projection morphogenesis	The process in which the anatomical structures of a neuron projection are generated and organized. A neuron projection is any process extending from a neural cell, such as axons or dendrites.
	GO:0018105	peptidyl-serine phosphorylation	The phosphorylation of peptidyl-serine to form peptidyl-O-phospho-L-serine.
	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:0030307	positive regulation of cell growth	Any process that activates or increases the frequency, rate, extent or direction of cell growth.
	GO:0050775	positive regulation of dendrite morphogenesis	Any process that activates or increases the frequency, rate or extent of dendrite morphogenesis.
	GO:0010765	positive regulation of sodium ion transport	Any process that increases the frequency, rate or extent of the directed movement of sodium ions (Na+) into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
	GO:0032411	positive regulation of transporter activity	Any process that activates or increases the activity of a transporter.
	GO:0006468	protein phosphorylation	The process of introducing a phosphate group on to a protein.
	GO:0042981	regulation of apoptotic process	Any process that modulates the occurrence or rate of cell death by apoptotic process.
	GO:0008217	regulation of blood pressure	Any process that modulates the force with which blood travels through the circulatory system. The process is controlled by a balance of processes that increase pressure and decrease pressure.
	GO:0050790	regulation of catalytic activity	Any process that modulates the activity of an enzyme.
	GO:0051726	regulation of cell cycle	Any process that modulates the rate or extent of progression through the cell cycle.
	GO:0001558	regulation of cell growth	Any process that modulates the frequency, rate, extent or direction of cell growth.
	GO:0030334	regulation of cell migration	Any process that modulates the frequency, rate or extent of cell migration.
	GO:0042127	regulation of cell proliferation	Any process that modulates the frequency, rate or extent of cell proliferation.
	GO:0060453	regulation of gastric acid secretion	Any process that modulates the rate frequency or extent of gastric secretion. Gastric secretion is the regulated release of gastric acid (hydrochloric acid) by parietal or oxyntic cells during digestion.
	GO:0051090	regulation of sequence-specific DNA binding transcription factor activity	Any process that modulates the frequency, rate or extent of the activity of a transcription factor, any factor involved in the initiation or regulation of transcription.
	GO:0070294	renal sodium ion absorption	A renal system process in which sodium ions are taken up from the collecting ducts and proximal and distal loops of the nephron. In non-mammalian species, absorption may occur in related structures.
	GO:0006950	response to 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 disturbance in organismal or cellular homeostasis, usually, but not necessarily, exogenous (e.g. temperature, humidity, ionizing radiation).
	GO:0006814	sodium ion transport	The directed movement of sodium ions (Na+) into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
	GO:0008542	visual learning	Any process in an organism in which a change in behavior of an individual occurs in response to repeated exposure to a visual cue.
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	GO:0005829	cytosol	The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
	GO:0005783	endoplasmic reticulum	The irregular network of unit membranes, visible only by electron microscopy, that occurs in the cytoplasm of many eukaryotic cells. The membranes form a complex meshwork of tubular channels, which are often expanded into slitlike cavities called cisternae. The ER takes two forms, rough (or granular), with ribosomes adhering to the outer surface, and smooth (with no ribosomes attached).
	GO:0005789	endoplasmic reticulum membrane	The lipid bilayer surrounding the endoplasmic reticulum.
	GO:0016020	membrane	A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
	GO:0005739	mitochondrion	A semiautonomous, self replicating organelle that occurs in varying numbers, shapes, and sizes in the cytoplasm of virtually all eukaryotic cells. It is notably the site of tissue respiration.
	GO:0043005	neuron projection	A prolongation or process extending from a nerve cell, e.g. an axon or dendrite.
	GO:0005654	nucleoplasm	That part of the nuclear content other than the chromosomes or the nucleolus.
	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:0048471	perinuclear region of cytoplasm	Cytoplasm situated near, or occurring around, the nucleus.
	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.

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	2r5t
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(no "Related Entries Specified in the PDB File" available for 2R5T)

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