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Asym./Biol. Unit (Jmol Viewer)

Asym./Biol. Unit - sites (Jmol Viewer)

Title :   STRUCTURAL ANALYSIS OF THE LYMPHOCYTE-SPECIFIC KINASE LCK IN COMPLEX WITH NON-SELECTIVE AND SRC FAMILY SELECTIVE KINASE INHIBITORS

Authors :   X. Zhu, J. L. Kim, P. E. Rose, D. R. Stover, L. M. Toledo, H. Zhao, K. A. Morgenstern

Date :   24 May 99 (Deposition) - 24 May 00 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.00

Chains :   Asym./Biol. Unit : A

Keywords :   Alpha Beta Fold, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   X. Zhu, J. L. Kim, J. R. Newcomb, P. E. Rose, D. R. Stover, L. M. Toledo, H. Zhao, K. A. Morgenstern
Structural Analysis Of The Lymphocyte-Specific Kinase Lck In Complex With Non-Selective And Src Family Selective Kinase Inhibitors.
Structure Fold. Des. V. 7 651 1999
PubMed-ID: 10404594 | Reference-DOI: 10.1016/S0969-2126(99)80086-0
(for further references see the PDB file header)

Molecule 1 - LCK KINASE
	Cell	:	LYMPHOCYTE
	Cellular Location	:	CYTOPLASM
	Chains	:	A
	EC Number	:	2.7.1.112
	Engineered	:	YES
	Expression System	:	TRICHOPLUSIA NI
	Expression System Cell	:	LYMPHOCYTE
	Expression System Common	:	CABBAGE LOOPER
	Expression System Taxid	:	7111
	Expression System Vector	:	BACULOVIRUS
	Fragment	:	CATALYTIC DOMAIN
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606

		1
Asymmetric/Biological Unit	:	A

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (3, 3)

No.	Name	Count	Type	Full Name
1	PTR	1	Mod. Amino Acid	O-PHOSPHOTYROSINE
2	SO4	1	Ligand/Ion	SULFATE ION
3	STU	1	Ligand/Ion	STAUROSPORINE

Asymmetric Unit (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	HOH A:37 , GLN A:298 , ARG A:299 , SER A:377 , LYS A:379 , TYR A:457 , ARG A:458 , ARG A:474	BINDING SITE FOR RESIDUE SO4 A 901
2	AC2	SOFTWARE	LEU A:251 , ALA A:271 , LYS A:273 , THR A:316 , GLU A:317 , TYR A:318 , MET A:319 , GLY A:322 , SER A:323 , ASP A:326 , ALA A:368 , LEU A:371	BINDING SITE FOR RESIDUE STU A 902

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

Asymmetric/Biological Unit

No.	Residues
1	Glu A:310	-	Pro A:311

Asymmetric/Biological Unit (3, 3)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_071291	L	341	P	LCK_HUMAN	Disease (IMD22)	587777335	A	L	341	P
2	UniProt	VAR_013465	A	353	V	LCK_HUMAN	Unclassified	---	A	A	353	V
3	UniProt	VAR_013466	P	447	L	LCK_HUMAN	Unclassified	---	A	P	447	L

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

Asymmetric/Biological Unit (2, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	PROTEIN_KINASE_ATP	PS00107	Protein kinases ATP-binding region signature.	LCK_HUMAN	251-273	1	A:251-273
2	PROTEIN_KINASE_TYR	PS00109	Tyrosine protein kinases specific active-site signature.	LCK_HUMAN	360-372	1	A:360-372

Asymmetric/Biological Unit (6, 6)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1a	ENST00000336890	1a	ENSE00001532907	chr1:32716840-32716972	133	LCK_HUMAN	-	0	0	-	-
1.2h	ENST00000336890	2h	ENSE00002175789	chr1:32739926-32740035	110	LCK_HUMAN	1-35	35	0	-	-
1.3a	ENST00000336890	3a	ENSE00001301511	chr1:32740338-32740419	82	LCK_HUMAN	36-63	28	0	-	-
1.3f	ENST00000336890	3f	ENSE00001323374	chr1:32740594-32740684	91	LCK_HUMAN	63-93	31	0	-	-
1.3h	ENST00000336890	3h	ENSE00001321874	chr1:32740922-32741020	99	LCK_HUMAN	93-126	34	0	-	-
1.4c	ENST00000336890	4c	ENSE00001299684	chr1:32741170-32741273	104	LCK_HUMAN	126-161	36	0	-	-
1.5	ENST00000336890	5	ENSE00001330813	chr1:32741515-32741664	150	LCK_HUMAN	161-211	51	0	-	-
1.6b	ENST00000336890	6b	ENSE00001307776	chr1:32741938-32742090	153	LCK_HUMAN	211-262	52	1	A:231-262	32
1.7a	ENST00000336890	7a	ENSE00001327737	chr1:32742208-32742387	180	LCK_HUMAN	262-322	61	1	A:262-322	61
1.8b	ENST00000336890	8b	ENSE00001292351	chr1:32745272-32745348	77	LCK_HUMAN	322-347	26	1	A:322-347	26
1.8e	ENST00000336890	8e	ENSE00001706218	chr1:32745442-32745595	154	LCK_HUMAN	348-399	52	1	A:348-399	52
1.9b	ENST00000336890	9b	ENSE00001805246	chr1:32745680-32745811	132	LCK_HUMAN	399-443	45	1	A:399-443	45
1.10d	ENST00000336890	10d	ENSE00001348148	chr1:32751115-32751766	652	LCK_HUMAN	443-509	67	1	A:443-502	60

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
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Chain A from PDB  Type:PROTEIN  Length:272
 aligned with LCK_HUMAN | P06239 from UniProtKB/Swiss-Prot  Length:509

    Alignment length:272
                                   240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450       460       470       480       490       500  
            LCK_HUMAN   231 KPWWEDEWEVPRETLKLVERLGAGQFGEVWMGYYNGHTKVAVKSLKQGSMSPDAFLAEANLMKQLQHQRLVRLYAVVTQEPIYIITEYMENGSLVDFLKTPSGIKLTINKLLDMAAQIAEGMAFIEERNYIHRDLRAANILVSDTLSCKIADFGLARLIEDNEYTAREGAKFPIKWTAPEAINYGTFTIKSDVWSFGILLTEIVTHGRIPYPGMTNPEVIQNLERGYRMVRPDNCPEELYQLMRLCWKERPEDRPTFDYLRSVLEDFFTATE 502
               SCOP domains d1qpda_ A: Lymphocyte kinase (lck)                                                                                                                                                                                                                                               SCOP domains
               CATH domains 1qpdA01 A:231-318 Phosphorylase Kinase; domain 1                                        1qpdA02 A:319-500 Transferase(Phosphotransferase) domain 1                                                                                                                            -- CATH domains
               Pfam domains --------------Pkinase_Tyr-1qpdA01 A:245-494                                                                                                                                                                                                                             -------- Pfam domains
         Sec.struct. author ..........hhh.eeeeeeeee...eeeeeeee...eeeeeeee.....hhhhhhhhhhhhhh........eeeee.....eeeee.....hhhhhh.hhhhhh.hhhhhhhhhhhhhhhhhhhhhh.ee....hhh.eee.....eee......ee..............hhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhh.........hhhhhhhhhhh..........hhhhhhhhhhhh..hhhhh.hhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------P-----------V---------------------------------------------------------------------------------------------L------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------PROTEIN_KINASE_ATP     --------------------------------------------------------------------------------------PROTEIN_KINAS---------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.6b  PDB: A:231-262       -----------------------------------------------------------Exon 1.8b  PDB: A:322-347 Exon 1.8e  PDB: A:348-399 UniProt: 348-399          -------------------------------------------Exon 1.10d  PDB: A:443-502 UniProt: 443-509 [INCOMPLETE]     Transcript 1 (1)
           Transcript 1 (2) -------------------------------Exon 1.7a  PDB: A:262-322 UniProt: 262-322                   ----------------------------------------------------------------------------Exon 1.9b  PDB: A:399-443 UniProt: 399-443   ----------------------------------------------------------- Transcript 1 (2)
                 1qpd A 231 KPWWEDAWEVPRETLKLVERLGAGQAGEVWMGYYNGHTKVAVKSLKQGSMSPDAFLAEANLMKQLQHQRLVRLYAVVTQEPIYIITEYMENGSLVDFLKTPSGIKLTINKLLDMAAQIAEGMAFIEERNYIHRDLRAANILVSDTLSCKIADFGLARLIEDAEyTAREGAKFPIKWTAPEAINYGTFTIKSDVWSFGILLTEIVTHGRIPYPGMTNPEVIQNLERGYRMVRPDNCPEELYQLMRLCWKERPEDRPTFDYLRSVLEDFFTATE 502
                                   240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390   |   400       410       420       430       440       450       460       470       480       490       500  
                                                                                                                                                                                             394-PTR

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

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: Alpha and beta proteins (a+b) (23004)

Fold: Protein kinase-like (PK-like) (2589)

Superfamily: Protein kinase-like (PK-like) (2589)

Family: Protein kinases, catalytic subunit (1977)

Protein domain: Lymphocyte kinase (lck) (34)

Human (Homo sapiens) [TaxId: 9606] (34)

d1qpda_

Asymmetric/Biological 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)

1qpdA01

A:231-318

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)

1qpdA02

A:319-500

Asymmetric/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: PKinase (934)

Family: Pkinase_Tyr (229)

Homo sapiens (Human) (202)

Pkinase_Tyr-1qpdA01

A:245-494

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (LCK_HUMAN | P06239)

molecular function
	GO:0005524	ATP binding	Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
	GO:0051117	ATPase binding	Interacting selectively and non-covalently with an ATPase, any enzyme that catalyzes the hydrolysis of ATP.
	GO:0042609	CD4 receptor binding	Interacting selectively and non-covalently with a CD4, a receptor found on the surface of T cells, monocytes and macrophages.
	GO:0042610	CD8 receptor binding	Interacting selectively and non-covalently with a CD8, a receptor found on the surface of thymocytes and cytotoxic and suppressor T-lymphocytes.
	GO:0042169	SH2 domain binding	Interacting selectively and non-covalently with a SH2 domain (Src homology 2) of a protein, a protein domain of about 100 amino-acid residues and belonging to the alpha + beta domain class.
	GO:0042802	identical protein binding	Interacting selectively and non-covalently with an identical protein or proteins.
	GO:0016301	kinase activity	Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule.
	GO:0004715	non-membrane spanning protein tyrosine kinase activity	Catalysis of the reaction: ATP + protein L-tyrosine = ADP + protein L-tyrosine phosphate by a non-membrane spanning protein.
	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:0043548	phosphatidylinositol 3-kinase binding	Interacting selectively and non-covalently with a phosphatidylinositol 3-kinase, any enzyme that catalyzes the addition of a phosphate group to an inositol lipid at the 3' position of the inositol ring.
	GO:0046934	phosphatidylinositol-4,5-bisphosphate 3-kinase activity	Catalysis of the reaction: 1-phosphatidyl-1D-myo-inositol 4,5-bisphosphate + ATP = a 1-phosphatidyl-1D-myo-inositol 3,4,5-trisphosphate + ADP + 2 H(+).
	GO:0008022	protein C-terminus binding	Interacting selectively and non-covalently with a protein C-terminus, the end of any peptide chain at which the 1-carboxy function of a constituent amino acid is not attached in peptide linkage to another amino-acid residue.
	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:0019901	protein kinase binding	Interacting selectively and non-covalently with a protein kinase, any enzyme that catalyzes the transfer of a phosphate group, usually from ATP, to a protein substrate.
	GO:0019903	protein phosphatase binding	Interacting selectively and non-covalently with any protein phosphatase.
	GO:0004722	protein serine/threonine phosphatase activity	Catalysis of the reaction: protein serine phosphate + H2O = protein serine + phosphate, and protein threonine phosphate + H2O = protein threonine + phosphate.
	GO:0004713	protein tyrosine kinase activity	Catalysis of the reaction: ATP + a protein tyrosine = ADP + protein tyrosine 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:0050853	B cell receptor signaling pathway	A series of molecular signals initiated by the cross-linking of an antigen receptor on a B cell.
	GO:0031295	T cell costimulation	The process of providing, via surface-bound receptor-ligand pairs, a second, antigen-independent, signal in addition to that provided by the T cell receptor to augment T cell activation.
	GO:0030217	T cell differentiation	The process in which a precursor cell type acquires characteristics of a more mature T-cell. A T cell is a type of lymphocyte whose definin characteristic is the expression of a T cell receptor complex.
	GO:0050852	T cell receptor signaling pathway	A series of molecular signals initiated by the cross-linking of an antigen receptor on a T cell.
	GO:0006919	activation of cysteine-type endopeptidase activity involved in apoptotic process	Any process that initiates the activity of the inactive enzyme cysteine-type endopeptidase in the context of an apoptotic process.
	GO:0006882	cellular zinc ion homeostasis	Any process involved in the maintenance of an internal steady state of zinc ions at the level of a cell.
	GO:0030097	hemopoiesis	The process whose specific outcome is the progression of the myeloid and lymphoid derived organ/tissue systems of the blood and other parts of the body over time, from formation to the mature structure. The site of hemopoiesis is variable during development, but occurs primarily in bone marrow or kidney in many adult vertebrates.
	GO:0045087	innate immune response	Innate immune responses are defense responses mediated by germline encoded components that directly recognize components of potential pathogens.
	GO:0050900	leukocyte migration	The movement of a leukocyte within or between different tissues and organs of the body.
	GO:0038083	peptidyl-tyrosine autophosphorylation	The phosphorylation by a protein of one or more of its own tyrosine amino acid residues, or a tyrosine residue on an identical protein.
	GO:0046854	phosphatidylinositol phosphorylation	The process of introducing one or more phosphate groups into a phosphatidylinositol, any glycerophosphoinositol having one phosphatidyl group esterified to one of the hydroxy groups of inositol.
	GO:0048015	phosphatidylinositol-mediated signaling	A series of molecular signals in which a cell uses a phosphatidylinositol-mediated signaling to convert a signal into a response. Phosphatidylinositols include phosphatidylinositol (PtdIns) and its phosphorylated derivatives.
	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:0030168	platelet activation	A series of progressive, overlapping events triggered by exposure of the platelets to subendothelial tissue. These events include shape change, adhesiveness, aggregation, and release reactions. When carried through to completion, these events lead to the formation of a stable hemostatic plug.
	GO:0050870	positive regulation of T cell activation	Any process that activates or increases the frequency, rate or extent of T cell activation.
	GO:0050862	positive regulation of T cell receptor signaling pathway	Any process that activates or increases the frequency, rate or extent of signaling pathways initiated by the cross-linking of an antigen receptor on a T cell.
	GO:2001244	positive regulation of intrinsic apoptotic signaling pathway	Any process that activates or increases the frequency, rate or extent of intrinsic apoptotic signaling pathway.
	GO:0006470	protein dephosphorylation	The process of removing one or more phosphoric residues from a protein.
	GO:0006468	protein phosphorylation	The process of introducing a phosphate group on to a protein.
	GO:0042127	regulation of cell proliferation	Any process that modulates the frequency, rate or extent of cell proliferation.
	GO:0050690	regulation of defense response to virus by virus	Any viral process that modulates the frequency, rate, or extent of the antiviral response of the host cell or organism.
	GO:0051249	regulation of lymphocyte activation	Any process that modulates the frequency, rate or extent of lymphocyte activation.
	GO:0014066	regulation of phosphatidylinositol 3-kinase signaling	Any process that modulates the frequency, rate or extent of signal transduction mediated by the phosphatidylinositol 3-kinase cascade.
	GO:0051209	release of sequestered calcium ion into cytosol	The process in which calcium ions sequestered in the endoplasmic reticulum, Golgi apparatus or mitochondria are released into the cytosolic compartment.
	GO:0042493	response to drug	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 drug stimulus. A drug is a substance used in the diagnosis, treatment or prevention of a disease.
	GO:0007169	transmembrane receptor protein tyrosine kinase signaling pathway	A series of molecular signals initiated by the binding of an extracellular ligand to a receptor on the surface of the target cell where the receptor possesses tyrosine kinase activity, and ending with regulation of a downstream cellular process, e.g. transcription.
	GO:0016032	viral process	A multi-organism process in which a virus is a participant. The other participant is the host. Includes infection of a host cell, replication of the viral genome, and assembly of progeny virus particles. In some cases the viral genetic material may integrate into the host genome and only subsequently, under particular circumstances, 'complete' its life cycle.
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:0070062	extracellular exosome	A vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. Extracellular exosomes, also simply called exosomes, have a diameter of about 40-100 nm.
	GO:0031234	extrinsic component of cytoplasmic side of plasma membrane	The component of a plasma membrane consisting of gene products and protein complexes that are loosely bound to its cytoplasmic surface, but not integrated into the hydrophobic region.
	GO:0001772	immunological synapse	An area of close contact between a lymphocyte (T-, B-, or natural killer cell) and a target cell formed through the clustering of particular signaling and adhesion molecules and their associated membrane rafts on both the lymphocyte and the target cell and facilitating activation of the lymphocyte, transfer of membrane from the target cell to the lymphocyte, and in some situations killing of the target cell through release of secretory granules and/or death-pathway ligand-receptor interaction.
	GO:0016020	membrane	A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
	GO:0045121	membrane raft	Any of the small (10-200 nm), heterogeneous, highly dynamic, sterol- and sphingolipid-enriched membrane domains that compartmentalize cellular processes. Small rafts can sometimes be stabilized to form larger platforms through protein-protein and protein-lipid interactions.
	GO:0000242	pericentriolar material	A network of small fibers that surrounds the centrioles in cells; contains the microtubule nucleating activity of the centrosome.
	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/Biological Unit
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	1qpd
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Description

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Ligands, Modified Residues, Ions (3, 3)

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SS Bonds (0, 0)

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