3CJA - JenaLib

Asym./Biol. Unit (Jmol Viewer)

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

Title :   STRUCTURE OF RATTUS NORVEGICUS NTPDASE2 IN COMPLEX WITH CALCIUM AND AMPPNP

Authors :   M. Zebisch, N. Strater

Date :   12 Mar 08 (Deposition) - 29 Apr 08 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.10

Chains :   Asym./Biol. Unit : A

Keywords :   Hydrolase, Alpha/Beta Protein, Actin-Like Fold, Alternative Splicing, Calcium, Glycoprotein, Magnesium, Membrane, Transmembrane (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   M. Zebisch, N. Strater
Structural Insight Into Signal Conversion And Inactivation By Ntpdase2 In Purinergic Signaling
Proc. Natl. Acad. Sci. Usa V. 105 6882 2008
PubMed-ID: 18458329 | Reference-DOI: 10.1073/PNAS.0802535105
(for further references see the PDB file header)

Molecule 1 - ECTONUCLEOSIDE TRIPHOSPHATE DIPHOSPHOHYDROLASE 2
	Chains	:	A
	EC Number	:	3.6.1.5
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET45B(+)
	Expression System Strain	:	ER2566
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Fragment	:	ECTODOMAIN, EXTRACELLULAR DOMAIN, UNP RESIDUES 29-461
	Gene	:	ENTPD2
	Organism Common	:	NORWAY RAT
	Organism Scientific	:	RATTUS NORVEGICUS
	Organism Taxid	:	10116
	Synonym	:	NTPDASE 2, ECTO-ATPASE, CD39 ANTIGEN-LIKE 1

		1
Asymmetric/Biological Unit	:	A

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (2, 2)

No.	Name	Count	Type	Full Name
1	ANP	1	Ligand/Ion	PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
2	CA	1	Ligand/Ion	CALCIUM ION

Asymmetric Unit (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	HOH A:505 , HOH A:506 , HOH A:507 , HOH A:508	BINDING SITE FOR RESIDUE CA A 502
2	AC2	SOFTWARE	GLY A:47 , SER A:48 , SER A:49 , HIS A:50 , THR A:122 , ALA A:123 , GLU A:165 , LEU A:202 , GLY A:203 , GLY A:204 , ALA A:205 , SER A:206 , ARG A:245 , ASP A:246 , SER A:346 , ALA A:347 , TYR A:350 , ARG A:394 , HOH A:503 , HOH A:504 , HOH A:506 , HOH A:510 , HOH A:624 , HOH A:718 , HOH A:777	BINDING SITE FOR RESIDUE ANP A 501

Asymmetric/Biological Unit

No.	Residues
1	A:75	-	A:99
2	A:242	-	A:284
3	A:265	-	A:310
4	A:323	-	A:328
5	A:377	-	A:399

Asymmetric/Biological Unit

No.	Residues
1	Arg A:191	-	Pro A:192

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

Asymmetric/Biological Unit (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	GDA1_CD39_NTPASE	PS01238	GDA1/CD39 family of nucleoside phosphatases signature.	ENTP2_RAT	160-175	1	A:160-175

(no "Exon" information available for 3CJA)

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:419
 aligned with ENTP2_RAT | O35795 from UniProtKB/Swiss-Prot  Length:495

    Alignment length:426
                                    45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375       385       395       405       415       425       435       445       455      
            ENTP2_RAT    36 PALKYGIVLDAGSSHTSMFVYKWPADKENDTGIVGQHSSCDVQGGGISSYANDPSKAGQSLVRCLEQALRDVPRDRHASTPLYLGATAGMRPFNLTSPEATARVLEAVTQTLTQYPFDFRGARILSGQDEGVFGWVTANYLLENFIKYGWVGRWIRPRKGTLGAMDLGGASTQITFETTSPSEDPGNEVHLRLYGQHYRVYTHSFLCYGRDQILLRLLASALQIHRFHPCWPKGYSTQVLLQEVYQSPCTMGQRPRAFNGSAIVSLSGTSNATLCRDLVSRLFNISSCPFSQCSFNGVFQPPVAGNFIAFSAFYYTVDFLTTVMGLPVGTLKQLEEATEITCNQTWTELQARVPGQKTRLADYCAVAMFIHQLLSRGYHFDERSFREVVFQKKAADTAVGWALGYMLNLTNLIPADLPGLRKGTHF 461
               SCOP domains d3cjaa1 A:36-178 NTPDase2                                                                                                                      d3cjaa2 A:179-461 NTPDase2                                                                                                                                                                                                                                                                  SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeeeeeeee....eeeeeeeee..........eeeeeee....hhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhh.eeeeeehhhhhhhhhhhhhhhhhhhhhhhhhhh....eeeeeee.hhhhhhhhhhhhhhhhh......ee..ee........eeeee...eeeeeee......hhh.eeeeee..eeeeeeeeeee..hhhhhhhhhhhhhhhhh..........eeeeehhhhhh.......-------..eeeee...hhhhhhhhhhh.........................eeeeehhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhh....hhhhhh.eee..ee..ee..hhhhhhhhhh......hhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------GDA1_CD39_NTPASE---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3cja A  36 PALKYGIVLDAGSSHTSMFVYKWPADKENDTGIVGQHSSCDVQGGGISSYANDPSKAGQSLVRCLEQALRDVPRDRHASTPLYLGATAGMRLLNLTSPEATARVLEAVTQTLTQYPFDFRGARILSGQDEGVFGWVTANYLLENFIKYGWVGRWIRPRKGTLGAMDLGGASTQITFETTSPSEDPGNEVHLRLYGQHYRVYTHSFLCYGRDQILLRLLASALQIHRFHPCWPKGYSTQVLLQEVYQSPCTMGQ-------SAIVSLSGTSNATLCRDLVSRLFNISSCPFSQCSFNGVFQPPVAGNFIAFSAFYYTVDFLTTVMGLPVGTLKQLEEATEITCNQTWTELQARVPGQKTRLADYCAVAMFIHQLLSRGYHFDERSFREVVFQKKAADTAVGWALGYMLNLTNLIPADLPGLRKGTHF 461
                                    45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285  |      -|      305       315       325       335       345       355       365       375       385       395       405       415       425       435       445       455      
                                                                                                                                                                                                                                                                                      288     296

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: Ribonuclease H-like motif (1424)

Superfamily: Actin-like ATPase domain (426)

Family: NTPDase (Nucleoside triphosphate diphosphohydrolase)-like (10)

Protein domain: NTPDase2 (4)

Norway rat (Rattus norvegicus) [TaxId: 10116] (4)

1a	d3cjaa1	A:36-178
1b	d3cjaa2	A:179-461

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

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

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (ENTP2_RAT | O35795)

molecular function
	GO:0005524	ATP binding	Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
	GO:0016887	ATPase activity	Catalysis of the reaction: ATP + H2O = ADP + phosphate + 2 H+. May or may not be coupled to another reaction.
	GO:0043262	adenosine-diphosphatase activity	Catalysis of the reaction: ADP + H2O = AMP + phosphate.
	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: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.
biological process
	GO:0035457	cellular response to interferon-alpha	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 an interferon-alpha stimulus. Interferon-alpha is a type I interferon.
	GO:0071354	cellular response to interleukin-6	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 an interleukin-6 stimulus.
	GO:0071222	cellular response to lipopolysaccharide	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 lipopolysaccharide stimulus; lipopolysaccharide is a major component of the cell wall of gram-negative bacteria.
	GO:0071356	cellular response to tumor necrosis factor	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 tumor necrosis factor stimulus.
	GO:0051260	protein homooligomerization	The process of creating protein oligomers, compounds composed of a small number, usually between three and ten, of identical component monomers. Oligomers may be formed by the polymerization of a number of monomers or the depolymerization of a large protein polymer.
	GO:0010996	response to auditory stimulus	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 an auditory stimulus.
cellular component
	GO:0044297	cell body	The portion of a cell bearing surface projections such as axons, dendrites, cilia, or flagella that includes the nucleus, but excludes all cell projections.
	GO:0031253	cell projection membrane	The portion of the plasma membrane surrounding a plasma membrane bounded cell surface projection.
	GO:0009986	cell surface	The external part of the cell wall and/or plasma membrane.
	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: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
		ANP	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		CA	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]

	Sites
		AC1	[ RasMol ]	+environment [ RasMol ]
		AC2	[ RasMol ]	+environment [ RasMol ]

	Cis Peptide Bonds
		Arg A:191 - Pro A:192	[ 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
	3cja
		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
	ENTP2_RAT \| O35795
		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)
	3.6.1.5
		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
	ENTP2_RAT \| O35795
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

UniProtKB/Swiss-Prot
	ENTP2_RAT \| O35795	:	3cj1 3cj7 3cj9 4bqz 4br0 4br2 4br5 4cd1 4cd3

3cj1	APO FORM
3cj7	AMP COMPLEX
3cj9	CA2+XAMPXPI COMPLEX

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 2)

Sites (2, 2)

SS Bonds (5, 5)

Cis Peptide Bonds (1, 1)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (1, 1)

Exons (0, 0)

Sequences/Alignments

Classification and Annotation

SCOP Domains (1, 2)

CATH Domains (0, 0)

Pfam Domains (0, 0)

Gene Ontology (18, 18)

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