2H03 - JenaLib

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Description

Title :   STRUCTURAL STUDIES OF PROTEIN TYROSINE PHOSPHATASE BETA CATALYTIC DOMAIN IN COMPLEX WITH INHIBITORS

Authors :   A. G. Evdokimov, M. E. Pokross, R. L. Walter, M. Mekel, J. L. Gray, K. G. Pe M. B. Maier, K. D. Amarasinghe, C. M. Clark, R. Nichols

Date :   13 May 06 (Deposition) - 13 Jun 06 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.65

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

Keywords :   Protein Tyrosine Phosphatase, Wpd-Loop, Sulfamic Acid, Phosphatase, Inhibitor, Drug Design, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   K. K. Amarasinghe, A. G. Evdokimov, K. Xu, C. M. Clark, M. B. Maier, A. Srivastava, A. O. Colson, G. S. Gerwe, G. E. Stake, B. W. Howard, M. E. Pokross, J. L. Gray, K. G. Peters
Design And Synthesis Of Potent, Non-Peptidic Inhibitors Of Hptpbeta.
Bioorg. Med. Chem. Lett. V. 16 4252 2006
PubMed-ID: 16759857 | Reference-DOI: 10.1016/J.BMCL.2006.05.074

Compounds

Molecule 1 - PROTEIN TYROSINE PHOSPHATASE, RECEPTOR TYPE, B,
	Chains	:	A
	EC Number	:	3.1.3.48
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PDEST-HISMBP
	Expression System Strain	:	TOP10
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Fragment	:	CATALYTIC DOMAIN, 1676-1970
	Gene	:	PTPRB
	Mutation	:	YES
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606

Structural Features

Chains, Units

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

Summary Information (see also Sequences/Alignments below)

Ligands, Modified Residues, Ions (3, 5)

Asymmetric Unit (3, 5)

No.	Name	Count	Type	Full Name
1	3UN	1	Ligand/Ion	(4-{4-[(TERT-BUTOXYCARBONYL)AMINO]-2,2-BIS(ETHOXYCARBONYL)BUTYL}PHENYL)SULFAMIC ACID
2	CL	2	Ligand/Ion	CHLORIDE ION
3	MG	2	Ligand/Ion	MAGNESIUM ION

Biological Unit 1 (1, 1)

No.	Name	Count	Type	Full Name
1	3UN	1	Ligand/Ion	(4-{4-[(TERT-BUTOXYCARBONYL)AMINO]-2,2-BIS(ETHOXYCARBONYL)BUTYL}PHENYL)SULFAMIC ACID
2	CL	-1	Ligand/Ion	CHLORIDE ION
3	MG	-1	Ligand/Ion	MAGNESIUM ION

Biological Unit 2 (1, 2)

No.	Name	Count	Type	Full Name
1	3UN	2	Ligand/Ion	(4-{4-[(TERT-BUTOXYCARBONYL)AMINO]-2,2-BIS(ETHOXYCARBONYL)BUTYL}PHENYL)SULFAMIC ACID
2	CL	-1	Ligand/Ion	CHLORIDE ION
3	MG	-1	Ligand/Ion	MAGNESIUM ION

Sites (5, 5)

Asymmetric Unit (5, 5)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	GLY A:1765 , ASN A:1766 , ASN A:1767 , PHE A:1768 , ARG A:1970	BINDING SITE FOR RESIDUE CL A 302
2	AC2	SOFTWARE	HOH A:56 , HOH A:57 , HOH A:74 , HOH A:76	BINDING SITE FOR RESIDUE MG A 303
3	AC3	SOFTWARE	HOH A:59 , HOH A:203 , HOH A:213 , HOH A:227 , ASP A:1827 , GLU A:1851	BINDING SITE FOR RESIDUE MG A 304
4	AC4	SOFTWARE	TYR A:1762 , PRO A:1764 , ARG A:1769 , ARG A:1770	BINDING SITE FOR RESIDUE CL A 305
5	AC5	SOFTWARE	HOH A:22 , ASP A:1720 , LEU A:1723 , TYR A:1733 , ASN A:1734 , ASN A:1735 , LYS A:1811 , ASP A:1870 , HIS A:1871 , CYS A:1904 , SER A:1905 , ALA A:1906 , GLY A:1907 , VAL A:1908 , GLY A:1909 , ARG A:1910 , HIS A:1945 , GLN A:1948	BINDING SITE FOR RESIDUE 3UN A 401

SS Bonds (0, 0)

(no "SS Bond" information available for 2H03)

Cis Peptide Bonds (0, 0)

(no "Cis Peptide Bond" information available for 2H03)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (1, 1)

Asymmetric Unit (1, 1)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_057139	G	1934	A	PTPRB_HUMAN	Polymorphism	17226367	A	G	1934	A

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

Biological Unit 1 (1, 1)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_057139	G	1934	A	PTPRB_HUMAN	Polymorphism	17226367	A	G	1934	A

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

Biological Unit 2 (1, 2)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_057139	G	1934	A	PTPRB_HUMAN	Polymorphism	17226367	A	G	1934	A

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

PROSITE Motifs (3, 3)

Asymmetric 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.	PTPRB_HUMAN	1703-1963	1	A:1703-1963
2	TYR_PHOSPHATASE_2	PS50056	Tyrosine specific protein phosphatases family profile.	PTPRB_HUMAN	1878-1954	1	A:1878-1954
3	TYR_PHOSPHATASE_1	PS00383	Tyrosine specific protein phosphatases active site.	PTPRB_HUMAN	1902-1912	1	A:1902-1912

Biological Unit 1 (3, 3)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	TYR_PHOSPHATASE_PTP	PS50055	PTP type protein phosphatase family profile.	PTPRB_HUMAN	1703-1963	1	A:1703-1963
2	TYR_PHOSPHATASE_2	PS50056	Tyrosine specific protein phosphatases family profile.	PTPRB_HUMAN	1878-1954	1	A:1878-1954
3	TYR_PHOSPHATASE_1	PS00383	Tyrosine specific protein phosphatases active site.	PTPRB_HUMAN	1902-1912	1	A:1902-1912

Biological Unit 2 (3, 6)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	TYR_PHOSPHATASE_PTP	PS50055	PTP type protein phosphatase family profile.	PTPRB_HUMAN	1703-1963	2	A:1703-1963
2	TYR_PHOSPHATASE_2	PS50056	Tyrosine specific protein phosphatases family profile.	PTPRB_HUMAN	1878-1954	2	A:1878-1954
3	TYR_PHOSPHATASE_1	PS00383	Tyrosine specific protein phosphatases active site.	PTPRB_HUMAN	1902-1912	2	A:1902-1912

Exons (9, 9)

Asymmetric Unit (9, 9)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.4a	ENST00000261266	4a	ENSE00000871974	chr12:71003624-71003541	84	PTPRB_HUMAN	1-18	18	0	-	-
1.5	ENST00000261266	5	ENSE00000871972	chr12:71003119-71002849	271	PTPRB_HUMAN	19-109	91	0	-	-
1.6	ENST00000261266	6	ENSE00001176717	chr12:70990107-70989829	279	PTPRB_HUMAN	109-202	94	0	-	-
1.7	ENST00000261266	7	ENSE00001176709	chr12:70988504-70988247	258	PTPRB_HUMAN	202-288	87	0	-	-
1.8	ENST00000261266	8	ENSE00001176702	chr12:70986325-70986062	264	PTPRB_HUMAN	288-376	89	0	-	-
1.9	ENST00000261266	9	ENSE00001176692	chr12:70984013-70983744	270	PTPRB_HUMAN	376-466	91	0	-	-
1.10	ENST00000261266	10	ENSE00001176680	chr12:70981047-70980787	261	PTPRB_HUMAN	466-553	88	0	-	-
1.11	ENST00000261266	11	ENSE00001176673	chr12:70975082-70974816	267	PTPRB_HUMAN	553-642	90	0	-	-
1.12	ENST00000261266	12	ENSE00001176665	chr12:70970425-70970162	264	PTPRB_HUMAN	642-730	89	0	-	-
1.13	ENST00000261266	13	ENSE00001176657	chr12:70965867-70965604	264	PTPRB_HUMAN	730-818	89	0	-	-
1.14	ENST00000261266	14	ENSE00001176650	chr12:70965069-70964806	264	PTPRB_HUMAN	818-906	89	0	-	-
1.15	ENST00000261266	15	ENSE00001176641	chr12:70963718-70963455	264	PTPRB_HUMAN	906-994	89	0	-	-
1.16	ENST00000261266	16	ENSE00001176634	chr12:70960484-70960215	270	PTPRB_HUMAN	994-1084	91	0	-	-
1.17	ENST00000261266	17	ENSE00001176624	chr12:70956887-70956624	264	PTPRB_HUMAN	1084-1172	89	0	-	-
1.18	ENST00000261266	18	ENSE00001176613	chr12:70954714-70954451	264	PTPRB_HUMAN	1172-1260	89	0	-	-
1.19	ENST00000261266	19	ENSE00001601030	chr12:70953404-70953123	282	PTPRB_HUMAN	1260-1354	95	0	-	-
1.20	ENST00000261266	20	ENSE00001754193	chr12:70949928-70949650	279	PTPRB_HUMAN	1354-1447	94	0	-	-
1.21a	ENST00000261266	21a	ENSE00001778550	chr12:70949089-70948940	150	PTPRB_HUMAN	1447-1497	51	0	-	-
1.22a	ENST00000261266	22a	ENSE00001618774	chr12:70946800-70946557	244	PTPRB_HUMAN	1497-1578	82	0	-	-
1.23	ENST00000261266	23	ENSE00001708455	chr12:70938443-70938337	107	PTPRB_HUMAN	1578-1614	37	0	-	-
1.24	ENST00000261266	24	ENSE00001782264	chr12:70934737-70934638	100	PTPRB_HUMAN	1614-1647	34	0	-	-
1.25	ENST00000261266	25	ENSE00001629388	chr12:70933802-70933719	84	PTPRB_HUMAN	1647-1675	29	0	-	-
1.26	ENST00000261266	26	ENSE00001617922	chr12:70933624-70933607	18	PTPRB_HUMAN	1675-1681	7	1	A:1678-1681	4
1.27	ENST00000261266	27	ENSE00001593093	chr12:70933486-70933405	82	PTPRB_HUMAN	1681-1708	28	1	A:1681-1708	28
1.28	ENST00000261266	28	ENSE00001711408	chr12:70932794-70932704	91	PTPRB_HUMAN	1709-1739	31	1	A:1709-1739	31
1.29	ENST00000261266	29	ENSE00001747568	chr12:70932011-70931935	77	PTPRB_HUMAN	1739-1764	26	1	A:1739-1764 (gaps)	26
1.30	ENST00000261266	30	ENSE00001708497	chr12:70929939-70929805	135	PTPRB_HUMAN	1765-1809	45	1	A:1765-1809	45
1.31	ENST00000261266	31	ENSE00001790021	chr12:70928735-70928613	123	PTPRB_HUMAN	1810-1850	41	1	A:1810-1850	41
1.32	ENST00000261266	32	ENSE00001778655	chr12:70928431-70928268	164	PTPRB_HUMAN	1851-1905	55	1	A:1851-1905	55
1.33	ENST00000261266	33	ENSE00001680441	chr12:70925950-70925815	136	PTPRB_HUMAN	1905-1950	46	1	A:1905-1950	46
1.34	ENST00000261266	34	ENSE00001754760	chr12:70918371-70918251	121	PTPRB_HUMAN	1951-1991	41	1	A:1951-1970	20
1.35	ENST00000261266	35	ENSE00001244013	chr12:70915291-70910630	4662	PTPRB_HUMAN	1991-1997	7	0	-	-

Sequences/Alignments

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:288
 aligned with PTPRB_HUMAN | P23467 from UniProtKB/Swiss-Prot  Length:1997

    Alignment length:293
                                  1687      1697      1707      1717      1727      1737      1747      1757      1767      1777      1787      1797      1807      1817      1827      1837      1847      1857      1867      1877      1887      1897      1907      1917      1927      1937      1947      1957      1967   
         PTPRB_HUMAN   1678 KTSCPIKINQFEGHFMKLQADSNYLLSKEYEELKDVGRNQSCDIALLPENRGKNRYNNILPYDATRVKLSNVDDDPCSDYINASYIPGNNFRREYIVTQGPLPGTKDDFWKMVWEQNVHNIVMVTQCVEKGRVKCDHYWPADQDSLYYGDLILQMLSESVLPEWTIREFKICGEEQLDAHRLIRHFHYTVWPDHGVPETTQSLIQFVRTVRDYINRSPGAGPTVVHCSAGVGRTGTFIALDRILQQLDSKDSVDIYGAVHDLRLHRVHMVQTECQYVYLHQCVRDVLRARKLR 1970
               SCOP domains d2h03a_ A: automated matches                                                                                                                                                                                                                                                                          SCOP domains
               CATH domains 2h03A00 A:1678-1970 Protein tyrosine phosphatase superfamily                                                                                                                                                                                                                                          CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....ee..hhhhhhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhh...........eee....-----..eeeeeee........eeee...hhhhhhhhhhhhhhh...eeee....ee..ee............eee..eeeeeeeeee...eeeeeeeeee..eeeeeeeeeeeee..........hhhhhhhhhhhhhhhhhh......eeee....hhhhhhhhhhhhhhhhhhhh.eehhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------A------------------------------------ SAPs(SNPs)
                PROSITE (1) -------------------------TYR_PHOSPHATASE_PTP  PDB: A:1703-1963 UniProt: 1703-1963                                                                                                                                                                                                             ------- PROSITE (1)
                PROSITE (2) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TYR_PHOSPHATASE_2  PDB: A:1878-1954 UniProt: 1878-1954                       ---------------- PROSITE (2)
                PROSITE (3) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TYR_PHOSPHA---------------------------------------------------------- PROSITE (3)
           Transcript 1 (1) 1.26---------------------------Exon 1.28  PDB: A:1709-1739    -------------------------Exon 1.30  PDB: A:1765-1809                  Exon 1.31  PDB: A:1810-1850              Exon 1.32  PDB: A:1851-1905 UniProt: 1851-1905         ---------------------------------------------Exon 1.34            Transcript 1 (1)
           Transcript 1 (2) ---Exon 1.27  PDB: A:1681-1708 ------------------------------Exon 1.29                 --------------------------------------------------------------------------------------------------------------------------------------------Exon 1.33  PDB: A:1905-1950 UniProt: 1905-1950-------------------- Transcript 1 (2)
                2h03 A 1678 KTSCPIKINQFEGHFMKLQADSNYLLSKEYEELKDVGRNQSCDIALLPENRGKNRYNNILPYDATRVKLSGG-----SDYINASYIPGNNFRREYIVTQGPLPGTKDDFWKMVWEQNVHNIVMVTQCVEKGRVKCDHYWPADQDSLYYGDLILQMLSESVLPEWTIREFKICGEEQLDAHRLIRHFHYTVWPDHGVPETTQSLIQFVRTVRDYINRSPGAGPTVVHCSAGVGRTGTFIALDRILQQLDSKDSVDIYGAVHDLRLHRVHMVQTECQYVYLHQCVRDVLRARKLR 1970
                                  1687      1697      1707      1717      1727      1737      1747 |    1757      1767      1777      1787      1797      1807      1817      1827      1837      1847      1857      1867      1877      1887      1897      1907      1917      1927      1937      1947      1957      1967   
                                                                                                1749  1755

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 '\|'

Classification and Annotation

SCOP Domains (1, 1)

Asymmetric 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: automated matches (83)

Protein domain: automated matches (83)

Human (Homo sapiens) [TaxId: 9606] (76)

d2h03a_

CATH Domains (1, 1)

Asymmetric 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)

2h03A00

A:1678-1970

Pfam Domains (0, 0)

(no "Pfam Domain" information available for 2H03)

Gene Ontology (15, 15)

Asymmetric Unit(hide GO term definitions)

Chain A (PTPRB_HUMAN | P23467)

molecular function
	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: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:0004725	protein tyrosine phosphatase activity	Catalysis of the reaction: protein tyrosine phosphate + H2O = protein tyrosine + phosphate.
	GO:0005001	transmembrane receptor protein tyrosine phosphatase activity	Combining with a signal and transmitting the signal from one side of the membrane to the other to initiate a change in cell activity by catalysis of the reaction: protein tyrosine phosphate + H2O = protein tyrosine + phosphate.
biological process
	GO:0001525	angiogenesis	Blood vessel formation when new vessels emerge from the proliferation of pre-existing blood vessels.
	GO:0016311	dephosphorylation	The process of removing one or more phosphoric (ester or anhydride) residues from a molecule.
	GO:0035335	peptidyl-tyrosine dephosphorylation	The removal of phosphoric residues from peptidyl-O-phospho-tyrosine to form peptidyl-tyrosine.
	GO:0006796	phosphate-containing compound metabolic process	The chemical reactions and pathways involving the phosphate group, the anion or salt of any phosphoric acid.
	GO:0006470	protein dephosphorylation	The process of removing one or more phosphoric residues from a protein.
cellular component
	GO:0016021	integral component of membrane	The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
	GO:0005887	integral component of plasma membrane	The component of the plasma membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
	GO:0016020	membrane	A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
	GO:0043235	receptor complex	Any protein complex that undergoes combination with a hormone, neurotransmitter, drug or intracellular messenger to initiate a change in cell function.

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	2h03
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	PTPRB_HUMAN \| P23467
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	3.1.3.48
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Related Entries

Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
	PTPRB_HUMAN \| P23467	:	2ahs 2h02 2h04 2hc1 2hc2 2i3r 2i3u 2i4e 2i4g 2i4h 2i5x

Related Entries Specified in the PDB File

2ho2	STRUCTURAL STUDIES OF PROTEIN TYROSINE PHOSPHATASE BETA CATALYTIC DOMAIN IN COMPLEX WITH INHIBITORS
2ho4	STRUCTURAL STUDIES OF PROTEIN TYROSINE PHOSPHATASE BETA CATALYTIC DOMAIN IN COMPLEX WITH INHIBITORS