2YD1 - JenaLib

Asym./Biol. Unit (Jmol Viewer)

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

Title :   CRYSTAL STRUCTURE OF THE N-TERMINAL IG1-2 MODULE OF DROSOPHILA RECEPTOR PROTEIN TYROSINE PHOSPHATASE DLAR

Authors :   C. H. Coles, Y. Shen, A. P. Tenney, C. Siebold, G. C. Sutton, W. Lu, J. T. Ga E. Y. Jones, J. G. Flanagan, A. R. Aricescu

Date :   17 Mar 11 (Deposition) - 13 Apr 11 (Release) - 04 May 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.80

Chains :   Asym./Biol. Unit : A

Keywords :   Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   C. H. Coles, Y. Shen, A. P. Tenney, C. Siebold, G. C. Sutton, W. Lu, J. T. Gallagher, E. Y. Jones, J. G. Flanagan, A. R. Aricescu
Proteoglycan-Specific Molecular Switch For Rptp Sigma Clustering And Neuronal Extension.
Science V. 332 484 2011
PubMed-ID: 21454754 | Reference-DOI: 10.1126/SCIENCE.1200840

Molecule 1 - TYROSINE-PROTEIN PHOSPHATASE LAR
	Chains	:	A
	EC Number	:	3.1.3.48
	Engineered	:	YES
	Expression System	:	HOMO SAPIENS
	Expression System Cell Line	:	HEK293T
	Expression System Common	:	HUMAN
	Expression System Taxid	:	9606
	Expression System Vector	:	PHLSEC
	Expression System Vector Type	:	PLASMID
	Fragment	:	IG1-2, RESIDUES 33-232
	Organism Common	:	FRUIT FLY
	Organism Scientific	:	DROSOPHILA MELANOGASTER
	Organism Taxid	:	7227
	Synonym	:	RECEPTOR PROTEIN TYROSINE PHOSPHATASE DLAR, PROTEIN-TYROSINE-PHOSPHATE PHOSPHOHYDROLASE, DLAR, RPTP

		1
Asymmetric/Biological Unit	:	A

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (1, 1)

No.	Name	Count	Type	Full Name
1	GLY	1	Mod. Amino Acid	GLYCINE

Asymmetric Unit (1, 1)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ARG A:40 , SER A:81 , ARG A:82 , ARG A:101 , ARG A:104 , LYS A:179	BINDING SITE FOR RESIDUE GLY A1230

Asymmetric/Biological Unit

No.	Residues
1	A:57	-	A:111
2	A:161	-	A:209

Asymmetric/Biological Unit

No.	Residues
1	Asp A:62	-	Pro A:63
2	Glu A:98	-	Pro A:99
3	Asn A:166	-	Pro A:167

(no "SAP(SNP)/Variant" information available for 2YD1)

(no "PROSITE Motif" information available for 2YD1)

(no "Exon" information available for 2YD1)

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
	(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:197
 aligned with LAR_DROME | P16621 from UniProtKB/Swiss-Prot  Length:2029

    Alignment length:216
                                    43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243      
           LAR_DROME     34 HPPEIIRKPQNQGVRVGGVASFYCAARGDPPPSIVWRKNGKKVSGTQSRYTVLEQPGGISILRIEPVRAGRDDAPYECVAENGVGDAVSADATLTIYEGDKTPAGFPVITQGPGTRVIEVGHTVLMTCKAIGNPTPNIYWIKNQTKVDMSNPRYSLKDGFLQIENSREEDQGKYECVAENSMGTEHSKATNLYVKVRRVPPTFSRPPETISEVMLG  249
               SCOP domains d2yd1a1 A:34-130 automated matches                                                               d2yd1a2 A:131-229 automated matches                                                                -------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
           Pfam domains (1) ----------------------------------------------------------------------------------------------------------I-set-2yd1A01 A:140-227                                                                 ---------------------- Pfam domains (1)
           Pfam domains (2) ----------------------------------------------------------------------------------------------------------I-set-2yd1A02 A:140-227                                                                 ---------------------- Pfam domains (2)
         Sec.struct. author ...eeee....eeee....eeeeeeee.....eeeeee..ee.......eeeeee...eeeeee..........eeeeeee.....eeeeeeeeeee..........eeee....eeee....eee..eee.....eeeeee..ee.......eeee..eeee...hhhhheeeeeeeee..eeee...eeeeee.-------------------. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                2yd1 A   34 HPPEIIRKPQNQGVRVGGVASFYCAARGDPPPSIVWRKNGKKVSGTQSRYTVLEQPGGISILRIEPVRAGRDDAPYECVAENGVGDAVSADATLTIYEGDKTPAGFPVITQGPGTRVIEVGHTVLMTCKAIGNPTPNIYWIKNQTKVDMSNPRYSLKDGFLQIENSREEDQGKYECVAENSMGTEHSKATNLYVKV-------------------G 1230
                                    43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223     |   -         -     |
                                                                                                                                                                                                                             229                1230

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: All beta proteins (24004)

Fold: Immunoglobulin-like beta-sandwich (7299)

Superfamily: Immunoglobulin (5995)

Family: automated matches (864)

Protein domain: automated matches (864)

Fruit fly (Drosophila melanogaster) [TaxId: 7227] (2)

1a	d2yd1a1	A:34-130
1b	d2yd1a2	A:131-229

(no "CATH Domain" information available for 2YD1)

Asymmetric/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: Ig (577)

Family: I-set (67)

Drosophila melanogaster (Fruit fly) (7)

1a	I-set-2yd1A01	A:140-227
1b	I-set-2yd1A02	A:140-227

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (LAR_DROME | P16621)

molecular function
	GO:0032093	SAM domain binding	Interacting selectively and non-covalently with a SAM (Sterile Alpha Motif) domain, which is a 70-amino acid protein sequence that participates in protein-protein, protein-lipid, and protein-RNA interactions and is conserved from lower to higher eukaryotes.
	GO:0008201	heparin binding	Interacting selectively and non-covalently with heparin, any member of a group of glycosaminoglycans found mainly as an intracellular component of mast cells and which consist predominantly of alternating alpha-(1->4)-linked D-galactose and N-acetyl-D-glucosamine-6-sulfate residues.
	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:0045467	R7 cell development	The process whose specific outcome is the progression of the R7 photoreceptor over time, from its formation to the mature structure. The R7 photoreceptor is the last photoreceptor to develop in the ommatidium.
	GO:0048675	axon extension	Long distance growth of a single axon process involved in cellular development.
	GO:0007411	axon guidance	The chemotaxis process that directs the migration of an axon growth cone to a specific target site in response to a combination of attractive and repulsive cues.
	GO:0007412	axon target recognition	The process in which an axon recognizes and binds to a set of cells with which it may form stable connections.
	GO:0007155	cell adhesion	The attachment of a cell, either to another cell or to an underlying substrate such as the extracellular matrix, via cell adhesion molecules.
	GO:0016311	dephosphorylation	The process of removing one or more phosphoric (ester or anhydride) residues from a molecule.
	GO:0001700	embryonic development via the syncytial blastoderm	The process whose specific outcome is the progression of the embryo over time, from zygote formation through syncytial blastoderm to the hatching of the first instar larva. An example of this process is found in Drosophila melanogaster.
	GO:0008045	motor neuron axon guidance	The process in which the migration of an axon growth cone of a motor neuron is directed to a specific target site in response to a combination of attractive and repulsive cues.
	GO:1903386	negative regulation of homophilic cell adhesion	Any process that stops, prevents or reduces the frequency, rate or extent of homophilic cell adhesion.
	GO:0007399	nervous system development	The process whose specific outcome is the progression of nervous tissue over time, from its formation to its mature state.
	GO:0048477	oogenesis	The complete process of formation and maturation of an ovum or female gamete from a primordial female germ cell. Examples of this process are found in Mus musculus and Drosophila melanogaster.
	GO:0035335	peptidyl-tyrosine dephosphorylation	The removal of phosphoric residues from peptidyl-O-phospho-tyrosine to form peptidyl-tyrosine.
	GO:0008594	photoreceptor cell morphogenesis	The process in which the structures of a photoreceptor cell are generated and organized. This process occurs while the initially relatively unspecialized cell is acquiring the specialized features of a photoreceptor cell, a sensory cell that reacts to the presence of light. An example of this is found in Drosophila melanogaster.
	GO:0006470	protein dephosphorylation	The process of removing one or more phosphoric residues from a protein.
	GO:0048841	regulation of axon extension involved in axon guidance	Any process that modulates the frequency, rate or extent of axon extension involved in axon guidance.
	GO:0008360	regulation of cell shape	Any process that modulates the surface configuration of a cell.
	GO:0031290	retinal ganglion cell axon guidance	The process in which the migration of an axon growth cone of a retinal ganglion cell (RGC) is directed to its target in the brain in response to a combination of attractive and repulsive cues.
	GO:0007283	spermatogenesis	The process of formation of spermatozoa, including spermatocytogenesis and spermiogenesis.
	GO:0051124	synaptic growth at neuromuscular junction	The growth of a synapse at a neuromuscular junction, the site of apposition of a motor end plate and the subneural cleft of the skeletal muscle fiber that it innervates.
cellular component
	GO:0030424	axon	The long process of a neuron that conducts nerve impulses, usually away from the cell body to the terminals and varicosities, which are sites of storage and release of neurotransmitter.
	GO:0005925	focal adhesion	Small region on the surface of a cell that anchors the cell to the extracellular matrix and that forms a point of termination of actin filaments.
	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:0016020	membrane	A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
	GO:0005875	microtubule associated complex	Any multimeric complex connected to a microtubule.
	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
	Complete Structure
		Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
		WebMol \| AstexViewer[tm]@PDBe (Java Applets, require no local installation except for Java; loading may be slow)
		STRAP (Java WebStart application, automatic local installation, requires Java; full application with system access!)
		RasMol (require local installation)
		Molscript (VRML) (requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)

	Ligands, Modified Residues, Ions
		GLY	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]

	Sites
		AC1	[ RasMol ]	+environment [ RasMol ]

	Cis Peptide Bonds
		Asn A:166 - Pro A:167	[ RasMol ]
		Asp A:62 - Pro A:63	[ RasMol ]
		Glu A:98 - Pro A:99	[ RasMol ]

Jmol
	protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick [ Asym./Biol. Unit PNG format \| Asym./Biol. Unit - sites PNG format ](automatic orientation, automatically generated)
Molscript
	protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick [ mono PDF format \| stereo PDF format ](default orientation, automatically generated)

Access by PDB/NDB ID
	2yd1
		Family and Domain Information	:	ProDom \| SYSTERS
		General Structural Information	:	GlycoscienceDB \| MMDB \| NDB \| OCA \| PDB \| PDBe \| PDBj \| PDBsum \| PDBWiki \| PQS \| PROTEOPEDIA
		Orientation in Membranes	:	OPM
		Protein Surface	:	SURFACE
		Secondary Structure	:	DSSP (structure derived) \| HSSP (homology derived)
		Structural Genomics	:	GeneCensus
		Structural Neighbours	:	CE \| VAST
		Structure Classification	:	CATH \| Dali \| SCOP
		Validation and Original Data	:	BMRB Data View \| BMRB Restraints Grid \| EDS \| PROCHECK \| RECOORD \| WHAT_CHECK

Access by UniProt ID/Accession number
	LAR_DROME \| P16621
		Comparative Protein Structure Models	:	ModBase
		Genomic Information	:	Ensembl
		Protein-protein Interaction	:	DIP
		Sequence, Family and Domain Information	:	InterPro \| Pfam \| SMART \| UniProtKB/SwissProt

Access by Enzyme Classificator (EC Number)
	3.1.3.48
		General Enzyme Information	:	BRENDA \| EC-PDB \| Enzyme \| IntEnz
		Pathway	:	KEGG \| MetaCyc

Access by Disease Identifier (MIM ID)
	(no 'MIM ID' available)
		Disease Information	:	OMIM

Access by GenAge ID
	(no 'GenAge ID' available)
		Age Related Information	:	GenAge

Access by PDB/NDB ID
		Domain Information	:	XDom
		Interatomic Contacts of Structural Units	:	CSU
		Ligand-protein Contacts	:	LPC
		Protein Cavities	:	castP
		Sequence and Secondary Structure	:	PDBCartoon
		Structure Alignment	:	STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
		Structure and Sequence Browser	:	STING

Access by UniProt ID/Accession number
	LAR_DROME \| P16621
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

UniProtKB/Swiss-Prot
	LAR_DROME \| P16621	:	3pxj

2yd2	CRYSTAL STRUCTURE OF THE N-TERMINAL IG1-2 MODULE OF HUMAN RECEPTOR PROTEIN TYROSINE PHOSPHATASE SIGMA
2yd3	CRYSTAL STRUCTURE OF THE N-TERMINAL IG1-2 MODULE OF HUMAN RECEPTOR PROTEIN TYROSINE PHOSPHATASE SIGMA
2yd4	CRYSTAL STRUCTURE OF THE N-TERMINAL IG1-2 MODULE OF CHICKEN RECEPTOR PROTEIN TYROSINE PHOSPHATASE SIGMA
2yd5	CRYSTAL STRUCTURE OF THE N-TERMINAL IG1-2 MODULE OF HUMAN RECEPTOR PROTEIN TYROSINE PHOSPHATASE LAR
2yd6	CRYSTAL STRUCTURE OF THE N-TERMINAL IG1-2 MODULE OF HUMAN RECEPTOR PROTEIN TYROSINE PHOSPHATASE DELTA
2yd7	CRYSTAL STRUCTURE OF THE N-TERMINAL IG1-2 MODULE OF HUMAN RECEPTOR PROTEIN TYROSINE PHOSPHATASE DELTA
2yd8	CRYSTAL STRUCTURE OF THE N-TERMINAL IG1-2 MODULE OF HUMAN RECEPTOR PROTEIN TYROSINE PHOSPHATASE LAR IN COMPLEX WITH SUCROSE OCTASULPHATE
2yd9	CRYSTAL STRUCTURE OF THE N-TERMINAL IG1-3 MODULE OF HUMAN RECEPTOR PROTEIN TYROSINE PHOSPHATASE SIGMA

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (1, 1)

Sites (1, 1)

SS Bonds (2, 2)

Cis Peptide Bonds (3, 3)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

Sequences/Alignments

Classification and Annotation

SCOP Domains (1, 2)

CATH Domains (0, 0)

Pfam Domains (1, 2)

Gene Ontology (33, 33)

Visualization

Interactive Views

Still Images

Databases and Analysis Tools

Databases

Analysis Tools

Related Entries

Entries Sharing at Least One Protein Chain (UniProt ID)

Related Entries Specified in the PDB File