2R7J - JenaLib

Title :   CRYSTAL STRUCTURE OF ROTAVIRUS NON STRUCTURAL PROTEIN NSP2 WITH H225A MUTATION

Authors :   M. Kumar, H. Jayaram, B. V. V. Prasad

Date :   09 Sep 07 (Deposition) - 23 Oct 07 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.60

Chains :   Asym. Unit : A
Biol. Unit 1: A  (8x)

Keywords :   Rotavirus, Ndp Kinase, Non Structural Protein, Ntpase, Rna Binding Protein, Rna-Binding (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   M. Kumar, H. Jayaram, R. Vasquez-Del Carpio, X. Jiang, Z. F. Taraporewala, R. H. Jacobson, J. T. Patton, B. V. V. Prasad
Crystallographic And Biochemical Analysis Of Rotavirus Nsp2 With Nucleotides Reveals A Nucleoside Diphosphate Kinase-Like Activity
J. Virol. V. 81 12272 2007
PubMed-ID: 17804496 | Reference-DOI: 10.1128/JVI.00984-07
(for further references see the PDB file header)

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (0, 0)

Sites (0, 0)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 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:307
 aligned with NSP2_ROTSR | Q03243 from UniProtKB/Swiss-Prot  Length:317

    Alignment length:311
                                    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       301       311 
           NSP2_ROTSR     2 AELACFCYPHLENDSYKFIPFNNLAIKAMLTAKVDKKDMDKFYDSIIYGIAPPPQFKKRYNTNDNSRGMNFETIMFTKVAMLICEALNSLKVTQANVSNVLSRVVSIRHLENLVIRKENPQDILFHSKDLLLKSTLIAIGQSKEIETTITAEGGEIVFQNAAFTMWKLTYLEHQLMPILDQNFIEYKVTLNEDKPISDVHVKELVAELRWQYNKFAVITHGKGHYRIVKYSSVANHADRVYATFKSNVKTGVNNDFNLLDQRIIWQNWYAFTSSMKQGNTLDVCKRLLFQKMKPEKNPFKGLSTDRKMDEV 312
               SCOP domains d2r7ja2 A:2-143 Rotavirus NSP2 fragment, N-terminal domain                                                                                    d2r7ja1 A:144-312 Rotavirus NSP2 fragment, C-terminal domain                                                                                                              SCOP domains
               CATH domains 2r7jA01 A:2-145 Rotavirus NSP2 fragment, N-terminal domain                                                                                      ------2r7jA02 A:152-312  [code=3.30.428.20, no name defined]                                                                                                            CATH domains
               Pfam domains Rota_NS35-2r7jA01 A:2-312                                                                                                                                                                                                                                                                                               Pfam domains
         Sec.struct. author .hhhh.eeeee....eeeee.hhhhhhhhh....hhhhh...ee.....ee.hhhhhhhh............hhhhhhhhhhhhhhhhh......hhhhhhhh..hhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhh.......hhhhh...eeeee...eeeee.hhhhh...........eeeeee......hhhhhhhhhhhhhhhh..eeeee.....eeeee..hhhhhhhhhhhhhhhhhhh..............hhhhhhhhhhhhh..hhhhhhhhhhh....----..hhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2r7j A   2 AELACFCYPHLENDSYKFIPFNNLAIKAMLTAKVDKKDMDKFYDSIIYGIAPPPQFKKRYNTNDNSRGMNFETIMFTKVAMLICEALNSLKVTQANVSNVLSRVVSIRHLENLVIRKENPQDILFHSKDLLLKSTLIAIGQSKEIETTITAEGGEIVFQNAAFTMWKLTYLEHQLMPILDQNFIEYKVTLNEDKPISDVHVKELVAELRWQYNKFAVITHGKGAYRIVKYSSVANHADRVYATFKSNVKTGVNNDFNLLDQRIIWQNWYAFTSSMKQGNTLDVCKRLLFQKMKP----FKGLSTDRKMDEV 312
                                    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   |   301       311 
                                                                                                                                                                                                                                                                                                                               295  300

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 (2, 2)

CATH Domains (2, 2)

Pfam Domains (1, 1)

Gene Ontology (7, 7)

Asymmetric Unit(hide GO term definitions)

Chain A (NSP2_ROTSR | Q03243)

molecular function
	GO:0003723	RNA binding	Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
	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:0016817	hydrolase activity, acting on acid anhydrides	Catalysis of the hydrolysis of any acid anhydride.
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	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:0019079	viral genome replication	Any process involved directly in viral genome replication, including viral nucleotide metabolism.
cellular component
	GO:0030430	host cell cytoplasm	The cytoplasm of a host cell.

Visualization

Interactive Views

Asymmetric 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
(no "Ligands, Modified Residues, Ions" information available for 2r7j)

	Sites
(no "Sites" information available for 2r7j)

	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 2r7j)

Biological Unit
	Complete Structure
		Biological Unit 1	[ Jena3D ]

Still Images

Databases and Analysis Tools

Databases

Access by PDB/NDB ID
	2r7j
		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
	NSP2_ROTSR \| Q03243
		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)
	(no 'Enzyme Classificator' available)
		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

Description