2VKQ - JenaLib

Title :   CRYSTAL STRUCTURE OF HUMAN CYTOSOLIC 5'-NUCLEOTIDASE III ( CN-III, NT5C3) IN COMPLEX WITH BERYLLIUM TRIFLUORIDE

Authors :   K. Wallden, M. Moche, C. H. Arrowsmith, H. Berglund, R. Busam, R. Collin L. G. Dahlgren, A. Edwards, S. Flodin, A. Flores, S. Graslund, M. Hamma M. D. Herman, A. Johansson, I. Johansson, A. Kallas, T. Karlberg, T. Ko L. Lehtio, M. E. Nilsson, T. Nyman, C. Persson, J. Sagemark, A. G. Thors L. Tresaugues, S. Van Den Berg, J. Weigelt, M. Welin, P. Nordlund, St Genomics Consortium (Sgc)

Date :   21 Dec 07 (Deposition) - 08 Jan 08 (Release) - 22 Apr 15 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.50

Chains :   Asym./Biol. Unit : A

Keywords :   Hydrolase, Nucleotidase, Disease Mutation, Hemolytic Anemia, Phosphotransferase, Nucleotide-Binding, Endoplasmic Reticulum, Nucleotide Metabolism (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   K. Wallden, P. Stenmark, S. Flodin, T. Nyman, M. Moche, M. Ehn, M. Hammarstrom, P. Nilsson-Ehle, P. Nordlund
Crystal Structure Of Human Cytosolic 5'- Nucleotidase Iii
To Be Published
PubMed: search
(for further references see the PDB file header)

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 2)

Sites (2, 2)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (8, 8)

PROSITE Motifs (0, 0)

Exons (8, 8)

Asymmetric/Biological Unit (8, 8)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1a	ENST00000242210	1a	ENSE00002172001	chr7:33102409-33102180	230	5NT3A_HUMAN	1-51	51	0	-	-
1.5b	ENST00000242210	5b	ENSE00001756142	chr7:33066527-33066429	99	5NT3A_HUMAN	52-84	33	1	A:14-34	21
1.6b	ENST00000242210	6b	ENSE00001650087	chr7:33063720-33063651	70	5NT3A_HUMAN	85-108	24	1	A:35-58	24
1.7a	ENST00000242210	7a	ENSE00001744550	chr7:33061711-33061665	47	5NT3A_HUMAN	108-123	16	1	A:58-73	16
1.8	ENST00000242210	8	ENSE00001625828	chr7:33060969-33060884	86	5NT3A_HUMAN	124-152	29	1	A:74-102	29
1.9	ENST00000242210	9	ENSE00001781106	chr7:33059336-33059247	90	5NT3A_HUMAN	152-182	31	1	A:102-132	31
1.10a	ENST00000242210	10a	ENSE00001601096	chr7:33057213-33057051	163	5NT3A_HUMAN	182-236	55	1	A:132-186	55
1.11b	ENST00000242210	11b	ENSE00001627659	chr7:33055482-33055282	201	5NT3A_HUMAN	237-303	67	1	A:187-253	67
1.12d	ENST00000242210	12d	ENSE00001938905	chr7:33054443-33053760	684	5NT3A_HUMAN	304-336	33	1	A:254-286	33

Sequences/Alignments

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:273
 aligned with 5NT3A_HUMAN | Q9H0P0 from UniProtKB/Swiss-Prot  Length:336

    Alignment length:273
                                    73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333   
          5NT3A_HUMAN    64 NPTRVEEIICGLIKGGAAKLQIITDFDMTLSRFSYKGKRCPTCHNIIDNCKLVTDECRKKLLQLKEKYYAIEVDPVLTVEEKYPYMVEWYTKSHGLLVQQALPKAKLKEIVAESDVMLKEGYENFFDKLQQHSIPVFIFSAGIGDVLEEVIRQAGVYHPNVKVVSNFMDFDETGVLKGFKGELIHVFNKHDGALRNTEYFNQLKDNSNIILLGDSQGDLRMADGVANVEHILKIGYLNDRVDELLEKYMDSYDIVLVQDESLEVANSILQKIL 336
               SCOP domains d2vkqa_ A: automated matches                                                                                                                                                                                                                                                      SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhh...eeeee.........ee..ee..hhhhhhhh....hhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhh.......hhhhhhhhhhhh...eeeeeeeehhhhhhhhhhh......eeeeee.eee.....eeee........hhhhhhhhhhhhhhh.....eeeeee..hhhhhh........eeeeeeee..hhhhhhhhhhh...eeee....hhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------G-----------------R-----------------------V-------------------------------------------P-------------------------R---------------------S--------------------------------------------------R----------------T--------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.5b            Exon 1.6b  PDB: A:35-58 ---------------Exon 1.8  PDB: A:74-102      -----------------------------Exon 1.10a  PDB: A:132-186 UniProt: 182-236            Exon 1.11b  PDB: A:187-253 UniProt: 237-303                        Exon 1.12d  PDB: A:254-286        Transcript 1 (1)
           Transcript 1 (2) --------------------------------------------Exon 1.7a       ----------------------------Exon 1.9  PDB: A:102-132       ---------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript 1 (2)
                 2vkq A  14 NPTRVEEIICGLIKGGAAKLQIITDFDMTLSRFSYKGKRCPTCHNIIDNCKLVTDECRKKLLQLKEKYYAIEVDPVLTVEEKYPYMVEWYTKSHGLLVQQALPKAKLKEIVAESDVMLKEGYENFFDKLQQHSIPVFIFSAGIGDVLEEVIRQAGVYHPNVKVVSNFMDFDETGVLKGFKGELIHVFNKHDGALRNTEYFNQLKDNSNIILLGDSQGDLRMADGVANVEHILKIGYLNDRVDELLEKYMDSYDIVLVQDESLEVANSILQKIL 286
                                    23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283

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)

CATH Domains (0, 0)

Pfam Domains (0, 0)

Gene Ontology (16, 16)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (5NT3A_HUMAN | Q9H0P0)

molecular function
	GO:0008665	2'-phosphotransferase activity	Catalysis of the transfer of a phosphate group from one compound to the 2' position of another.
	GO:0008253	5'-nucleotidase activity	Catalysis of the reaction: a 5'-ribonucleotide + H2O = a ribonucleoside + 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:0000287	magnesium ion binding	Interacting selectively and non-covalently with magnesium (Mg) ions.
	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.
	GO:0016740	transferase activity	Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
biological process
	GO:0046085	adenosine metabolic process	The chemical reactions and pathways involving adenosine, adenine riboside, a ribonucleoside found widely distributed in cells of every type as the free nucleoside and in combination in nucleic acids and various nucleoside coenzymes.
	GO:0016311	dephosphorylation	The process of removing one or more phosphoric (ester or anhydride) residues from a molecule.
	GO:0009117	nucleotide metabolic process	The chemical reactions and pathways involving a nucleotide, a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the glycose moiety; may be mono-, di- or triphosphate; this definition includes cyclic nucleotides (nucleoside cyclic phosphates).
	GO:0046135	pyrimidine nucleoside catabolic process	The chemical reactions and pathways resulting in the breakdown of one of a family of organic molecules consisting of a pyrimidine base covalently bonded to a sugar ribose (a ribonucleoside) or deoxyribose (a deoxyribonucleoside).
	GO:0006213	pyrimidine nucleoside metabolic process	The chemical reactions and pathways involving any pyrimidine nucleoside, one of a family of organic molecules consisting of a pyrimidine base covalently bonded to ribose (a ribonucleoside) or deoxyribose (a deoxyribonucleoside).
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	GO:0005829	cytosol	The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
	GO:0005783	endoplasmic reticulum	The irregular network of unit membranes, visible only by electron microscopy, that occurs in the cytoplasm of many eukaryotic cells. The membranes form a complex meshwork of tubular channels, which are often expanded into slitlike cavities called cisternae. The ER takes two forms, rough (or granular), with ribosomes adhering to the outer surface, and smooth (with no ribosomes attached).
	GO:0005739	mitochondrion	A semiautonomous, self replicating organelle that occurs in varying numbers, shapes, and sizes in the cytoplasm of virtually all eukaryotic cells. It is notably the site of tissue respiration.

Visualization

Interactive Views

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
		BEF	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		MG	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]

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

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

Still Images

Databases and Analysis Tools

Databases

Access by PDB/NDB ID
	2vkq
		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
	5NT3A_HUMAN \| Q9H0P0
		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)
	3.1.3.5
		General Enzyme Information	:	BRENDA \| EC-PDB \| Enzyme \| IntEnz
		Pathway	:	KEGG \| MetaCyc

Access by Disease Identifier (MIM ID)
	266120
		Disease Information	:	OMIM

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

Description