1PXH - JenaLib

Asym./Biol. Unit (Jmol Viewer)

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Title :   CRYSTAL STRUCTURE OF PROTEIN TYROSINE PHOSPHATASE 1B WITH POTENT AND SELECTIVE BIDENTATE INHIBITOR COMPOUND 2

Authors :   J. P. Sun, A. Fedorov, S. Y. Lee, X. L. Guo, K. Shen, D. S. Lawrence, S. C. Almo, Z. Y. Zhang

Date :   04 Jul 03 (Deposition) - 12 Aug 03 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.15

Chains :   Asym./Biol. Unit : A

Keywords :   Protein Tyrosine Phosphatase, Ptp1B, Phosphatase Inhibitor, X-Ray Diffraction, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   J. P. Sun, A. A. Fedorov, S. Y. Lee, X. L. Guo, K. Shen, D. S. Lawrence, S. C. Almo, Z. Y. Zhang
Crystal Structure Of Ptp1B Complexed With A Potent And Selective Bidentate Inhibitor.
J. Biol. Chem. V. 278 12406 2003
PubMed-ID: 12547827 | Reference-DOI: 10.1074/JBC.M212491200
(for further references see the PDB file header)

Molecule 1 - PROTEIN-TYROSINE PHOSPHATASE, NON-RECEPTOR TYPE 1
	Chains	:	A
	EC Number	:	3.1.3.48
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21(DE3)
	Expression System Plasmid	:	PUC118
	Expression System Strain	:	BL21 (DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Fragment	:	RESIDUES 1-321
	Gene	:	PTP1B
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	PROTEIN-TYROSINE PHOSPHATASE 1B, PTP-1B

		1
Asymmetric/Biological Unit	:	A

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (3, 5)

No.	Name	Count	Type	Full Name
1	ACY	2	Ligand/Ion	ACETIC ACID
2	MG	2	Ligand/Ion	MAGNESIUM ION
3	SNA	1	Ligand/Ion	N-{1-[5-(1-CARBAMOYL-2-MERCAPTO-ETHYLCARBAMOYL)-PENTYLCARBAMOYL]-2-[4-(DIFLUORO-PHOSPHONO-METHYL)-PHENYL]-ETHYL}-3-{2-[4-(DIFLUORO-PHOSPHONO-METHYL)-PHENYL]-ACETYLAMINO}-SUCCINAMIC ACID

Asymmetric Unit (5, 5)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	HOH A:605 , HOH A:606 , HOH A:607 , HOH A:608 , HOH A:609	BINDING SITE FOR RESIDUE MG A 322
2	AC2	SOFTWARE	HOH A:529 , HOH A:540 , HOH A:542	BINDING SITE FOR RESIDUE MG A 323
3	AC3	SOFTWARE	LYS A:5 , LYS A:41 , TYR A:46 , ARG A:47 , ASP A:48 , ASP A:181 , PHE A:182 , CYS A:215 , SER A:216 , ALA A:217 , GLY A:218 , ILE A:219 , GLY A:220 , ARG A:221 , GLN A:262 , HOH A:570 , HOH A:604	BINDING SITE FOR RESIDUE SNA A 401
4	AC4	SOFTWARE	ARG A:79 , SER A:205 , HOH A:517 , HOH A:528	BINDING SITE FOR RESIDUE ACY A 402
5	AC5	SOFTWARE	GLU A:76 , LEU A:234 , LYS A:248 , HOH A:566	BINDING SITE FOR RESIDUE ACY A 403

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

(no "Cis Peptide Bond" information available for 1PXH)

(no "SAP(SNP)/Variant" information available for 1PXH)

Asymmetric/Biological Unit (3, 3)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	TYR_PHOSPHATASE_PTP	PS50055	PTP type protein phosphatase family profile.	PTN1_HUMAN	3-277	1	A:3-277
2	TYR_PHOSPHATASE_2	PS50056	Tyrosine specific protein phosphatases family profile.	PTN1_HUMAN	189-268	1	A:189-268
3	TYR_PHOSPHATASE_1	PS00383	Tyrosine specific protein phosphatases active site.	PTN1_HUMAN	213-223	1	A:213-223

Asymmetric/Biological Unit (8, 8)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1	ENST00000371621	1	ENSE00001455721	chr20:49126891-49127127	237	PTN1_HUMAN	1-21	21	1	A:2-21	20
1.2	ENST00000371621	2	ENSE00000509635	chr20:49177900-49177990	91	PTN1_HUMAN	22-52	31	1	A:22-52	31
1.3	ENST00000371621	3	ENSE00000662794	chr20:49181506-49181606	101	PTN1_HUMAN	52-85	34	1	A:52-85	34
1.4	ENST00000371621	4	ENSE00000662795	chr20:49184917-49185015	99	PTN1_HUMAN	86-118	33	1	A:86-118	33
1.5	ENST00000371621	5	ENSE00000662796	chr20:49191054-49191191	138	PTN1_HUMAN	119-164	46	1	A:119-164	46
1.6	ENST00000371621	6	ENSE00000662797	chr20:49194957-49195166	210	PTN1_HUMAN	165-234	70	1	A:165-234	70
1.7	ENST00000371621	7	ENSE00000662798	chr20:49195705-49195866	162	PTN1_HUMAN	235-288	54	1	A:235-288	54
1.8	ENST00000371621	8	ENSE00000662799	chr20:49196240-49196463	224	PTN1_HUMAN	289-363	75	1	A:289-298	10
1.9	ENST00000371621	9	ENSE00001172461	chr20:49197802-49197997	196	PTN1_HUMAN	363-428	66	0	-	-
1.10	ENST00000371621	10	ENSE00001455694	chr20:49199229-49201299	2071	PTN1_HUMAN	429-435	7	0	-	-

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:297
 aligned with PTN1_HUMAN | P18031 from UniProtKB/Swiss-Prot  Length:435

    Alignment length:297
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       
           PTN1_HUMAN     2 EMEKEFEQIDKSGSWAAIYQDIRHEASDFPCRVAKLPKNKNRNRYRDVSPFDHSRIKLHQEDNDYINASLIKMEEAQRSYILTQGPLPNTCGHFWEMVWEQKSRGVVMLNRVMEKGSLKCAQYWPQKEEKEMIFEDTNLKLTLISEDIKSYYTVRQLELENLTTQETREILHFHYTTWPDFGVPESPASFLNFLFKVRESGSLSPEHGPVVVHCSAGIGRSGTFCLADTCLLLMDKRKDPSSVDIKKVLLEMRKFRMGLIQTADQLRFSYLAVIEGAKFIMGDSSVQDQWKELSHED 298
               SCOP domains d1pxha_ A: Tyrosine phosphatase                                                                                                                                                                                                                                                                           SCOP domains
               CATH domains 1pxhA00 A:2-298 Protein tyrosine phosphatase superfamily                                                                                                                                                                                                                                                  CATH domains
               Pfam domains --------------------------------------Y_phosphatase-1pxhA01 A:40-276                                                                                                                                                                                                               ---------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhhh.........hhhhhhhh...........eee.......eeeeeeeee....eeeeee......hhhhhhhhhhhh...eeee.......................eee....eeeeeeeeee...eeeeeeeeee.....eeeeeeeee..........hhhhhhhhhhhhhhh.........eeee.....hhhhhhhhhhhhhhhhhhh......hhhhhhhhhh........hhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) -TYR_PHOSPHATASE_PTP  PDB: A:3-277 UniProt: 3-277                                                                                                                                                                                                                                   --------------------- PROSITE (1)
                PROSITE (2) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TYR_PHOSPHATASE_2  PDB: A:189-268 UniProt: 189-268                              ------------------------------ PROSITE (2)
                PROSITE (3) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TYR_PHOSPHA--------------------------------------------------------------------------- PROSITE (3)
           Transcript 1 (1) Exon 1.1  PDB: A:2-2Exon 1.2  PDB: A:22-52         ---------------------------------Exon 1.4  PDB: A:86-118          Exon 1.5  PDB: A:119-164 UniProt: 119-164     Exon 1.6  PDB: A:165-234 UniProt: 165-234                             Exon 1.7  PDB: A:235-288 UniProt: 235-288             Exon 1.8   Transcript 1 (1)
           Transcript 1 (2) --------------------------------------------------Exon 1.3  PDB: A:52-85            --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript 1 (2)
                 1pxh A   2 EMEKEFEQIDKSGSWAAIYQDIRHEASDFPCRVAKLPKNKNRNRYRDVSPFDHSRIKLHQEDNDYINASLIKMEEAQRSYILTQGPLPNTCGHFWEMVWEQKSRGVVMLNRVMEKGSLKCAQYWPQKEEKEMIFEDTNLKLTLISEDIKSYYTVRQLELENLTTQETREILHFHYTTWPDFGVPESPASFLNFLFKVRESGSLSPEHGPVVVHCSAGIGRSGTFCLADTCLLLMDKRKDPSSVDIKKVLLEMRKFRMGLIQTADQLRFSYLAVIEGAKFIMGDSSVQDQWKELSHED 298
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291

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) (23833)

Fold: (Phosphotyrosine protein) phosphatases II (296)

Superfamily: (Phosphotyrosine protein) phosphatases II (296)

Family: Higher-molecular-weight phosphotyrosine protein phosphatases (166)

Protein domain: Tyrosine phosphatase (120)

Human (Homo sapiens), 1B [TaxId: 9606] (111)

d1pxha_

Asymmetric/Biological Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: Alpha-Beta Complex (3881)

Topology: Protein-Tyrosine Phosphatase; Chain A (262)

Homologous Superfamily: Protein tyrosine phosphatase superfamily (228)

Human (Homo sapiens) (196)

1pxhA00

A:2-298

Asymmetric/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: Phosphatase (121)

Family: Y_phosphatase (93)

Homo sapiens (Human) (82)

Y_phosphatase-1pxhA01

A:40-276

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (PTN1_HUMAN | P18031)

molecular function
	GO:0019899	enzyme binding	Interacting selectively and non-covalently with any enzyme.
	GO:0046875	ephrin receptor binding	Interacting selectively and non-covalently with an ephrin receptor.
	GO:0016787	hydrolase activity	Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
	GO:0005158	insulin receptor binding	Interacting selectively and non-covalently with the insulin receptor.
	GO:0016791	phosphatase activity	Catalysis of the hydrolysis of phosphoric monoesters, releasing inorganic phosphate.
	GO:0004721	phosphoprotein phosphatase activity	Catalysis of the reaction: a phosphoprotein + H2O = a protein + phosphate. Together with protein kinases, these enzymes control the state of phosphorylation of cell proteins and thereby provide an important mechanism for regulating cellular activity.
	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: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:0051721	protein phosphatase 2A binding	Interacting selectively and non-covalently with the enzyme protein phosphatase 2A.
	GO:0004725	protein tyrosine phosphatase activity	Catalysis of the reaction: protein tyrosine phosphate + H2O = protein tyrosine + phosphate.
	GO:0030971	receptor tyrosine kinase binding	Interacting selectively and non-covalently with a receptor that possesses protein tyrosine kinase activity.
	GO:0008270	zinc ion binding	Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
	GO:0036498	IRE1-mediated unfolded protein response	A series of molecular signals mediated by the endoplasmic reticulum stress sensor IRE1 (Inositol-requiring transmembrane kinase/endonuclease). Begins with activation of IRE1 in response to endoplasmic reticulum (ER) stress, and ends with regulation of a downstream cellular process, e.g. transcription. One target of activated IRE1 is the transcription factor HAC1 in yeast, or XBP1 in mammals; IRE1 cleaves an intron of a mRNA coding for HAC1/XBP1 to generate an activated HAC1/XBP1 transcription factor, which controls the up regulation of UPR-related genes. At least in mammals, IRE1 can also signal through additional intracellular pathways including JNK and NF-kappaB.
	GO:0060397	JAK-STAT cascade involved in growth hormone signaling pathway	The process in which STAT proteins (Signal Transducers and Activators of Transcription) are activated by members of the JAK (janus activated kinase) family of tyrosine kinases, following the binding of physiological ligands to the growth hormone receptor. Once activated, STATs dimerize and translocate to the nucleus and modulate the expression of target genes.
	GO:0031532	actin cytoskeleton reorganization	A process that is carried out at the cellular level which results in dynamic structural changes to the arrangement of constituent parts of cytoskeletal structures comprising actin filaments and their associated proteins.
	GO:0007257	activation of JUN kinase activity	The initiation of the activity of the inactive enzyme JUN kinase (JNK).
	GO:0016311	dephosphorylation	The process of removing one or more phosphoric (ester or anhydride) residues from a molecule.
	GO:0030968	endoplasmic reticulum unfolded protein response	The series of molecular signals generated as a consequence of the presence of unfolded proteins in the endoplasmic reticulum (ER) or other ER-related stress; results in changes in the regulation of transcription and translation.
	GO:0008286	insulin receptor signaling pathway	The series of molecular signals generated as a consequence of the insulin receptor binding to insulin.
	GO:0070373	negative regulation of ERK1 and ERK2 cascade	Any process that stops, prevents, or reduces the frequency, rate or extent of signal transduction mediated by the ERK1 and ERK2 cascade.
	GO:0043407	negative regulation of MAP kinase activity	Any process that stops, prevents, or reduces the frequency, rate or extent of MAP kinase activity.
	GO:1903898	negative regulation of PERK-mediated unfolded protein response	Any process that stops, prevents or reduces the frequency, rate or extent of the PERK-mediated unfolded protein response.
	GO:1902236	negative regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway	Any process that stops, prevents or reduces the frequency, rate or extent of an endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway.
	GO:0046627	negative regulation of insulin receptor signaling pathway	Any process that stops, prevents, or reduces the frequency, rate or extent of insulin receptor signaling.
	GO:0009968	negative regulation of signal transduction	Any process that stops, prevents, or reduces the frequency, rate or extent of signal transduction.
	GO:0030948	negative regulation of vascular endothelial growth factor receptor signaling pathway	Any process that stops, prevents, or reduces the frequency, rate or extent of vascular endothelial growth factor receptor signaling pathway activity.
	GO:0006987	obsolete activation of signaling protein activity involved in unfolded protein response	OBSOLETE. The conversion of a specific protein, possessing protein kinase and endoribonuclease activities, to an active form as a result of signaling via the unfolded protein response.
	GO:0035335	peptidyl-tyrosine dephosphorylation	The removal of phosphoric residues from peptidyl-O-phospho-tyrosine to form peptidyl-tyrosine.
	GO:1990264	peptidyl-tyrosine dephosphorylation involved in inactivation of protein kinase activity	Any peptidyl-tyrosine dephosphorylation that is involved in inactivation of protein kinase activity.
	GO:0035791	platelet-derived growth factor receptor-beta signaling pathway	A series of molecular signals initiated by the binding of a ligand to a beta-type platelet-derived growth factor receptor (PDGFbeta) on the surface of a signal-receiving cell, and ending with regulation of a downstream cellular process, e.g. transcription.
	GO:1903896	positive regulation of IRE1-mediated unfolded protein response	Any process that activates or increases the frequency, rate or extent of the IRE1-mediated unfolded protein response.
	GO:0061098	positive regulation of protein tyrosine kinase activity	Any process that increases the rate, frequency, or extent of protein tyrosine kinase activity.
	GO:2000646	positive regulation of receptor catabolic process	Any process that activates or increases the frequency, rate or extent of receptor catabolic process.
	GO:0006470	protein dephosphorylation	The process of removing one or more phosphoric residues from a protein.
	GO:0030100	regulation of endocytosis	Any process that modulates the frequency, rate or extent of endocytosis.
	GO:1902202	regulation of hepatocyte growth factor receptor signaling pathway	Any process that modulates the frequency, rate or extent of hepatocyte growth factor receptor signaling pathway.
	GO:0046626	regulation of insulin receptor signaling pathway	Any process that modulates the frequency, rate or extent of insulin receptor signaling.
	GO:0033157	regulation of intracellular protein transport	Any process that modulates the frequency, rate or extent of the directed movement of proteins within cells.
	GO:0009966	regulation of signal transduction	Any process that modulates the frequency, rate or extent of signal transduction.
	GO:0060338	regulation of type I interferon-mediated signaling pathway	Any process that modulates the rate, frequency or extent of a type I interferon-mediated signaling pathway. A type I interferon-mediated signaling pathway is the series of molecular events generated as a consequence of a type I interferon binding to a cell surface receptor.
	GO:0034976	response to endoplasmic reticulum stress	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 stress acting at the endoplasmic reticulum. ER stress usually results from the accumulation of unfolded or misfolded proteins in the ER lumen.
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	GO:0098554	cytoplasmic side of endoplasmic reticulum membrane	The side (leaflet) of the plasma membrane that faces the cytoplasm.
	GO:0031410	cytoplasmic vesicle	A vesicle found in the cytoplasm of a cell.
	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:0005769	early endosome	A membrane-bounded organelle that receives incoming material from primary endocytic vesicles that have been generated by clathrin-dependent and clathrin-independent endocytosis; vesicles fuse with the early endosome to deliver cargo for sorting into recycling or degradation pathways.
	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: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.
	GO:0097443	sorting endosome	A multivesicular body surrounded by and connected with multiple tubular compartments with associated vesicles.

Asymmetric/Biological Unit
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	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 1pxh)

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	1pxh
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1n6w	1N6W IS THE SAME PROTEIN COMPLEX WITH THE SAME INHIBITOR. HOWEVER THE INHIBITOR WAS REFINED WITH SEVERAL DISTORTED COVALENT ANGLES.

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Ligands, Modified Residues, Ions (3, 5)

Sites (5, 5)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

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Exons (8, 8)

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