3QCF - JenaLib

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Biological Unit 2 (Jmol Viewer)

Title :   HUMAN RECEPTOR PROTEIN TYROSINE PHOSPHATASE GAMMA, DOMAIN 1, IN COMPLEX WITH 3-[(3,4-DICHLOROBENZYL)SULFANYL]THIOPHENE-2-CARBOXYLIC ACID VIA CO-CRYSTALLIZATION

Authors :   S. Sheriff

Date :   16 Jan 11 (Deposition) - 28 Dec 11 (Release) - 28 Dec 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.50

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

Keywords :   Tyrosine Receptor Phosphatase, Twisted Mixed Beta-Sheets Flanked By {Alpha}-Helices, Hydrolase-Hydrolase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   S. Sheriff, B. R. Beno, W. Zhai, W. A. Kostich, P. A. Mcdonnell, K. Kish, V. Goldfarb, M. Gao, S. E. Kiefer, J. Yanchunas, Y. Huang, S. Shi, S. Zhu C. Dzierba, J. Bronson, J. E. Macor, K. K. Appiah, R. S. Westphal, J. O'Connell, S. W. Gerritz
Small Molecule Receptor Protein Tyrosine Phosphatase [Gamma](Rptp[Gamma]) Ligands That Inhibit Phosphatase Activity Via Perturbation Of The Tryptophan-Proline-Aspartate (Wpd) Loop
J. Med. Chem. V. 54 6548 2011
PubMed-ID: 21882820 | Reference-DOI: 10.1021/JM2003766
(for further references see the PDB file header)

Molecule 1 - RECEPTOR-TYPE TYROSINE-PROTEIN PHOSPHATASE GAMMA
	Chains	:	A, B
	EC Number	:	3.1.3.48
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET28
	Expression System Strain	:	ROSETTA(DE3)
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	PTPG, PTPRG
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	PROTEIN-TYROSINE PHOSPHATASE GAMMA, R-PTP-GAMMA

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 3)

No.	Name	Count	Type	Full Name
1	NXY	2	Ligand/Ion	3-[(3,4-DICHLOROBENZYL)SULFANYL]THIOPHENE-2-CARBOXYLICACID
2	SO4	1	Ligand/Ion	SULFATE ION

Biological Unit 1 (1, 1)

No.	Name	Count	Type	Full Name
1	NXY	1	Ligand/Ion	3-[(3,4-DICHLOROBENZYL)SULFANYL]THIOPHENE-2-CARBOXYLICACID
2	SO4	-1	Ligand/Ion	SULFATE ION

Biological Unit 2 (2, 2)

No.	Name	Count	Type	Full Name
1	NXY	1	Ligand/Ion	3-[(3,4-DICHLOROBENZYL)SULFANYL]THIOPHENE-2-CARBOXYLICACID
2	SO4	1	Ligand/Ion	SULFATE ION

Asymmetric Unit (3, 3)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ILE A:950 , TYR A:1023 , TRP A:1026 , GLY A:1030 , VAL A:1031 , PRO A:1032 , VAL A:1038 , PHE A:1041 , ARG A:1066 , TYR A:1070 , GLU A:1107 , GLN A:1108 , PHE A:1111	BINDING SITE FOR RESIDUE NXY A 2001
2	AC2	SOFTWARE	ILE B:950 , TYR B:1023 , TRP B:1026 , VAL B:1031 , VAL B:1038 , PHE B:1041 , ARG B:1066 , TYR B:1070 , GLN B:1108 , PHE B:1111	BINDING SITE FOR RESIDUE NXY B 2001
3	AC3	SOFTWARE	SER A:982 , LYS A:984 , ARG A:993 , LYS B:981 , ARG B:993	BINDING SITE FOR RESIDUE SO4 B 2051

(no "SS Bond" information available for 3QCF)

Asymmetric Unit

No.	Residues
1	Pro B:1051	-	Glu B:1052

(no "SAP(SNP)/Variant" information available for 3QCF)

Asymmetric Unit (3, 6)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	TYR_PHOSPHATASE_PTP	PS50055	PTP type protein phosphatase family profile.	PTPRG_HUMAN	848-1119 1150-1410	2	A:848-1119 B:848-1119 -
2	TYR_PHOSPHATASE_2	PS50056	Tyrosine specific protein phosphatases family profile.	PTPRG_HUMAN	1036-1110 1327-1401	2	A:1036-1110 B:1036-1110 -
3	TYR_PHOSPHATASE_1	PS00383	Tyrosine specific protein phosphatases active site.	PTPRG_HUMAN	1058-1068	2	A:1058-1068 B:1058-1068

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.	PTPRG_HUMAN	848-1119 1150-1410	1	A:848-1119 - -
2	TYR_PHOSPHATASE_2	PS50056	Tyrosine specific protein phosphatases family profile.	PTPRG_HUMAN	1036-1110 1327-1401	1	A:1036-1110 - -
3	TYR_PHOSPHATASE_1	PS00383	Tyrosine specific protein phosphatases active site.	PTPRG_HUMAN	1058-1068	1	A:1058-1068 -

Biological Unit 2 (3, 3)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	TYR_PHOSPHATASE_PTP	PS50055	PTP type protein phosphatase family profile.	PTPRG_HUMAN	848-1119 1150-1410	1	- B:848-1119 -
2	TYR_PHOSPHATASE_2	PS50056	Tyrosine specific protein phosphatases family profile.	PTPRG_HUMAN	1036-1110 1327-1401	1	- B:1036-1110 -
3	TYR_PHOSPHATASE_1	PS00383	Tyrosine specific protein phosphatases active site.	PTPRG_HUMAN	1058-1068	1	- B:1058-1068

(no "Exon" information available for 3QCF)

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:284
 aligned with PTPRG_HUMAN | P23470 from UniProtKB/Swiss-Prot  Length:1445

    Alignment length:299
                                   834       844       854       864       874       884       894       904       914       924       934       944       954       964       974       984       994      1004      1014      1024      1034      1044      1054      1064      1074      1084      1094      1104      1114         
         PTPRG_HUMAN    825 MEAIPVKQFVKHIGELYSNNQHGFSEDFEEVQRCTADMNITAEHSNHPENKHKNRYINILAYDHSRVKLRPLPGKDSKHSDYINANYVDGYNKAKAYIATQGPLKSTFEDFWRMIWEQNTGIIVMITNLVEKGRRKCDQYWPTENSEEYGNIIVTLKSTKIHACYTVRRFSIRNTKVKKGQKGNPKGRQNERVVIQYHYTQWPDMGVPEYALPVLTFVRRSSAARMPETGPVLVHCSAGVGRTGTYIVIDSMLQQIKDKSTVNVLGFLKHIRTQRNYLVQTEEQYIFIHDALLEAILGK 1123
               SCOP domains d3qcfa_ A: automated matches                                                                                                                                                                                                                                                                                SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eehhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhh...........eee......--.....eeeeeeeee..eeeeeeee...hhhhhhhhhhhhhhhh..eeee....ee..ee..........eeee..eeeeeeeeee...eeeeeeeeee..-------------..eeeeeeee...........hhhhhhhhhhhhhh.......eeee....hhhhhhhhhhhhhhhhhhhhheehhhhhhhhhh........hhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) -----------------------TYR_PHOSPHATASE_PTP  PDB: A:848-1119 UniProt: 848-1119                                                                                                                                                                                                                          ---- PROSITE (1)
                PROSITE (2) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TYR_PHOSPHATASE_2  PDB: A:1036-1110 UniProt: 1036-1110                     ------------- PROSITE (2)
                PROSITE (3) -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TYR_PHOSPHA------------------------------------------------------- PROSITE (3)
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                3qcf A  825 MEAIPVKQFVKHIGELYSNNQHGFSEDFEEVQRCTADMNITAEHSNHPENKHKNRYINILAYDHSRVKLRPLPG--SKHSDYINANYVDGYNKAKAYIATQGPLKSTFEDFWRMIWEQNTGIIVMITNLVEKGRRKCDQYWPTENSEEYGNIIVTLKSTKIHACYTVRRFSIRNTK-------------NERVVIQYHYTQWPDMGVPEYALPVLTFVRRSSAARMPETGPVLVHCSAGVGRTGTYIVIDSMLQQIKDKSTVNVLGFLKHIRTQRNYLVQTEEQYIFIHDALLEAILGK 1123
                                   834       844       854       864       874       884       894   |  |904       914       924       934       944       954       964       974       984       994     |   -      1014      1024      1034      1044      1054      1064      1074      1084      1094      1104      1114         
                                                                                                   898  |                                                                                               1000          1014                                                                                                             
                                                                                                      901

Chain B from PDB  Type:PROTEIN  Length:284
 aligned with PTPRG_HUMAN | P23470 from UniProtKB/Swiss-Prot  Length:1445

    Alignment length:298
                                   834       844       854       864       874       884       894       904       914       924       934       944       954       964       974       984       994      1004      1014      1024      1034      1044      1054      1064      1074      1084      1094      1104      1114        
         PTPRG_HUMAN    825 MEAIPVKQFVKHIGELYSNNQHGFSEDFEEVQRCTADMNITAEHSNHPENKHKNRYINILAYDHSRVKLRPLPGKDSKHSDYINANYVDGYNKAKAYIATQGPLKSTFEDFWRMIWEQNTGIIVMITNLVEKGRRKCDQYWPTENSEEYGNIIVTLKSTKIHACYTVRRFSIRNTKVKKGQKGNPKGRQNERVVIQYHYTQWPDMGVPEYALPVLTFVRRSSAARMPETGPVLVHCSAGVGRTGTYIVIDSMLQQIKDKSTVNVLGFLKHIRTQRNYLVQTEEQYIFIHDALLEAILG 1122
               SCOP domains d3qcfb_ B: automated matches                                                                                                                                                                                                                                                                               SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhh..hhhhh...........eee.......-.....eeeeeeeee..eeeeeeee...hhhhhhhhhhhhhhh...eeee....ee..ee..........eeee..eeeeeeeeee...eeeeeeeeee..-------------..eeeeeeee...........hhhhhhhhhhhhhh.......eeee....hhhhhhhhhhhhhhhhhhhhheehhhhhhhhhhh.......hhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) -----------------------TYR_PHOSPHATASE_PTP  PDB: B:848-1119 UniProt: 848-1119                                                                                                                                                                                                                          --- PROSITE (1)
                PROSITE (2) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TYR_PHOSPHATASE_2  PDB: B:1036-1110 UniProt: 1036-1110                     ------------ PROSITE (2)
                PROSITE (3) -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TYR_PHOSPHA------------------------------------------------------ PROSITE (3)
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                3qcf B  825 MEAIPVKQFVKHIGELYSNNQHGFSEDFEEVQRCTADMNITAEHSNHPENKHKNRYINILAYDHSRVKLRPLPGK-SKHSDYINANYVDGYNKAKAYIATQGPLKSTFEDFWRMIWEQNTGIIVMITNLVEKGRRKCDQYWPTENSEEYGNIIVTLKSTKIHACYTVRRFSIRNTK-------------NERVVIQYHYTQWPDMGVPEYALPVLTFVRRSSAARMPETGPVLVHCSAGVGRTGTYIVIDSMLQQIKDKSTVNVLGFLKHIRTQRNYLVQTEEQYIFIHDALLEAILG 1122
                                   834       844       854       864       874       884       894    | |904       914       924       934       944       954       964       974       984       994     |   -      1014      1024      1034      1044      1054      1064      1074      1084      1094      1104      1114        
                                                                                                    899 |                                                                                               1000          1014                                                                                                            
                                                                                                      901

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 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)

1a	d3qcfa_	A:
1b	d3qcfb_	B:

(no "CATH Domain" information available for 3QCF)

(no "Pfam Domain" information available for 3QCF)

Asymmetric Unit(hide GO term definitions)

Chain A,B (PTPRG_HUMAN | P23470)

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:0042802	identical protein binding	Interacting selectively and non-covalently with an identical protein or proteins.
	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:0016311	dephosphorylation	The process of removing one or more phosphoric (ester or anhydride) residues from a molecule.
	GO:0010633	negative regulation of epithelial cell migration	Any process that stops, prevents, or reduces the frequency, rate or extent of epithelial cell migration.
	GO:0035335	peptidyl-tyrosine dephosphorylation	The removal of phosphoric residues from peptidyl-O-phospho-tyrosine to form peptidyl-tyrosine.
	GO:0006470	protein dephosphorylation	The process of removing one or more phosphoric residues from a protein.
	GO:1903385	regulation of homophilic cell adhesion	Any process that modulates the frequency, rate or extent of homophilic cell adhesion.
	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.
cellular component
	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: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.

Asymmetric Unit
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		Pro B:1051 - Glu B:1052	[ RasMol ]

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	3qcf
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Ligands, Modified Residues, Ions (2, 3)

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