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(-) Description

Title :  CRYSTAL STRUCTURE OF THE D52N VARIANT OF CYTOSOLIC 5'-NUCLEOTIDASE II IN COMPLEX WITH INOSINE MONOPHOSPHATE AND 2,3-BISPHOSPHOGLYCERATE
 
Authors :  K. Wallden, P. Nordlund
Date :  26 Apr 10  (Deposition) - 16 Mar 11  (Release) - 20 Jul 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (4x)
Keywords :  Hydrolase, Metal-Binding, Nucleotide Metabolism (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  K. Wallden, P. Nordlund
Structural Basis For The Allosteric Regulation And Substrate Recognition Of Human Cytosolic 5'-Nucleotidase Ii
J. Mol. Biol. V. 408 684 2011
PubMed-ID: 21396942  |  Reference-DOI: 10.1016/J.JMB.2011.02.059

(-) Compounds

Molecule 1 - CYTOSOLIC PURINE 5'-NUCLEOTIDASE
    ChainsA
    EC Number3.1.3.5
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    Expression System VariantR3 PRARE2
    Expression System VectorP28A-LIC
    Expression System Vector TypePLASMID
    MutationYES
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymCYTOSOLIC 5'-NUCLEOTIDASE II

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit A
Biological Unit 1 (4x)A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 4)

Asymmetric Unit (4, 4)
No.NameCountTypeFull Name
1DG21Ligand/Ion(2R)-2,3-DIPHOSPHOGLYCERIC ACID
2GOL1Ligand/IonGLYCEROL
3IMP1Ligand/IonINOSINIC ACID
4MG1Ligand/IonMAGNESIUM ION
Biological Unit 1 (3, 12)
No.NameCountTypeFull Name
1DG24Ligand/Ion(2R)-2,3-DIPHOSPHOGLYCERIC ACID
2GOL4Ligand/IonGLYCEROL
3IMP4Ligand/IonINOSINIC ACID
4MG-1Ligand/IonMAGNESIUM ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:144 , LYS A:362 , ARG A:456 , TYR A:457BINDING SITE FOR RESIDUE DG2 A1489
2AC2SOFTWAREPHE A:283 , ASP A:284 , LEU A:285 , ILE A:286 , GLN A:322 , GLY A:324 , ILE A:325 , HOH A:2256BINDING SITE FOR RESIDUE GOL A1490
3AC3SOFTWAREASN A:52 , MET A:53 , ASP A:54 , PHE A:157 , ARG A:202 , ASP A:206 , HIS A:209 , TYR A:210 , LYS A:215 , THR A:249 , ASN A:250 , SER A:251 , LYS A:292 , MG A:1492 , HOH A:2107 , HOH A:2215 , HOH A:2218 , HOH A:2257BINDING SITE FOR RESIDUE IMP A1491
4AC4SOFTWAREASN A:52 , ASP A:54 , ASP A:351 , IMP A:1491 , HOH A:2215 , HOH A:2218BINDING SITE FOR RESIDUE MG A1492

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2XCV)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Ser A:62 -Pro A:63
2Lys A:292 -Pro A:293

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (2, 2)

Asymmetric Unit (2, 2)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_024244T3A5NTC_HUMANPolymorphism10883841AT3A
2UniProtVAR_030242Q136R5NTC_HUMANPolymorphism12262171AQ136R

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
Biological Unit 1 (2, 8)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_024244T3A5NTC_HUMANPolymorphism10883841AT3A
2UniProtVAR_030242Q136R5NTC_HUMANPolymorphism12262171AQ136R

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (17, 17)

Asymmetric Unit (17, 17)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1aENST000003432891aENSE00001759705chr10:104953056-104952993645NTC_HUMAN-00--
1.3ENST000003432893ENSE00002186305chr10:104934739-1049346151255NTC_HUMAN1-34341A:3-3432
1.6ENST000003432896ENSE00001787725chr10:104899236-104899163745NTC_HUMAN34-59261A:34-5926
1.8aENST000003432898aENSE00001707803chr10:104866463-1048663461185NTC_HUMAN59-98401A:59-9840
1.9aENST000003432899aENSE00001645482chr10:104865558-104865463965NTC_HUMAN98-130331A:98-13033
1.11ENST0000034328911ENSE00001742963chr10:104861083-104860992925NTC_HUMAN130-161321A:130-16132
1.12ENST0000034328912ENSE00001739246chr10:104860859-104860802585NTC_HUMAN161-180201A:161-18020
1.15ENST0000034328915ENSE00001753876chr10:104859776-104859683945NTC_HUMAN180-211321A:180-21132
1.16aENST0000034328916aENSE00001705007chr10:104858741-104858688545NTC_HUMAN212-229181A:212-22918
1.18bENST0000034328918bENSE00002152144chr10:104857131-104857048845NTC_HUMAN230-257281A:230-25728
1.19ENST0000034328919ENSE00001748493chr10:104855737-104855696425NTC_HUMAN258-271141A:258-27114
1.20bENST0000034328920bENSE00001646238chr10:104854212-1048541051085NTC_HUMAN272-307361A:272-30736
1.21aENST0000034328921aENSE00001596497chr10:104853795-104853729675NTC_HUMAN308-330231A:308-33023
1.22ENST0000034328922ENSE00001711453chr10:104853066-1048528961715NTC_HUMAN330-387581A:330-38758
1.23ENST0000034328923ENSE00001659728chr10:104851372-104851321525NTC_HUMAN387-404181A:387-39610
1.24ENST0000034328924ENSE00001610324chr10:104850753-104850693615NTC_HUMAN404-424211A:421-4244
1.25ENST0000034328925ENSE00001778811chr10:104850544-1048503681775NTC_HUMAN425-483591A:425-48359
1.26dENST0000034328926dENSE00001648268chr10:104849665-10484594037265NTC_HUMAN484-561781A:484-4885

(-) 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:462
 aligned with 5NTC_HUMAN | P49902 from UniProtKB/Swiss-Prot  Length:561

    Alignment length:486
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402       412       422       432       442       452       462       472       482      
           5NTC_HUMAN     3 TSWSDRLQNAADMPANMDKHALKKYRREAYHRVFVNRSLAMEKIKCFGFDMDYTLAVYKSPEYESLGFELTVERLVSIGYPQELLSFAYDSTFPTRGLVFDTLYGNLLKVDAYGNLLVCAHGFNFIRGPETREQYPNKFIQRDDTERFYILNTLFNLPETYLLACLVDFFTNCPRYTSCETGFKDGDLFMSYRSMFQDVRDAVDWVHYKGSLKEKTVENLEKYVVKDGKLPLLLSRMKEVGKVFLATNSDYKYTDKIMTYLFDFPHGPKPGSSHRPWQSYFDLILVDARKPLFFGEGTVLRQVDTKTGKLKIGTYTGPLQHGIVYSGGSSDTICDLLGAKGKDILYIGDHIFGDILKSKKRQGWRTFLVIPELAQELHVWTDKSSLFEELQSLDIFLAELYKHLDSSSNERPDISSIQRRIKKVTHDMDMCYGMMGSLFRSGSRQTLFASQVMRYADLYAASFINLLYYPFSYLFRAAHVLMPHES 488
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains --------------------------------5_nucleotid-2xcvA01 A:35-488                                                                                                                                                                                                                                                                                                                                                                                                                                           Pfam domains
         Sec.struct. author .hhhhhhhhhhhh....hhhhhhhhhhhhhhh.ee...ee.hhh.eeee...........hhhhhhhhhhhhhhhhhh..hhhhhhh..........eeee....eeeee.....eeeeee..eeehhhhhhhhh............eeee.hhhhhhhhhhhhhhhhhhhhh...eee..eeee..eeeehhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhh....hhhhhhhhhhhhheeeee...hhhhhhhhhhhhh.............hhhhhh.eeee....hhhhh....eeee....................eeee.hhhhhhhhh..hhh.eeeee.hhhhhhhhhhhhhh.eeeee..hhhhhhhhhhhhhhhhhhhhhhh------------------------hhhhhhhhhhhhh........ee..eehhhhhhhhhhh.eee.hhhhhhhh....ee......hhhhh Sec.struct. author
                 SAPs(SNPs) A------------------------------------------------------------------------------------------------------------------------------------R---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
           Transcript 1 (1) Exon 1.3  PDB: A:3-34           ------------------------Exon 1.8a  PDB: A:59-98 UniProt: 59-98  -------------------------------Exon 1.11  PDB: A:130-161       ------------------Exon 1.15  PDB: A:180-211       Exon 1.16a        Exon 1.18b  PDB: A:230-257  Exon 1.19     Exon 1.20b  PDB: A:272-307          Exon 1.21a             --------------------------------------------------------Exon 1.23         --------------------Exon 1.25  PDB: A:425-483 UniProt: 425-483                 1.26d Transcript 1 (1)
           Transcript 1 (2) -------------------------------Exon 1.6  PDB: A:34-59    --------------------------------------Exon 1.9a  PDB: A:98-130         ------------------------------Exon 1.12           -----------------------------------------------------------------------------------------------------------------------------------------------------Exon 1.22  PDB: A:330-387 UniProt: 330-387                ----------------Exon 1.24            ---------------------------------------------------------------- Transcript 1 (2)
                 2xcv A   3 TSWSDRLQNAADMPANMDKHALKKYRREAYHRVFVNRSLAMEKIKCFGFNMDYTLAVYKSPEYESLGFELTVERLVSIGYPQELLSFAYDSTFPTRGLVFDTLYGNLLKVDAYGNLLVCAHGFNFIRGPETREQYPNKFIQRDDTERFYILNTLFNLPETYLLACLVDFFTNCPRYTSCETGFKDGDLFMSYRSMFQDVRDAVDWVHYKGSLKEKTVENLEKYVVKDGKLPLLLSRMKEVGKVFLATNSDYKYTDKIMTYLFDFPHGPKPGSSHRPWQSYFDLILVDARKPLFFGEGTVLRQVDTKTGKLKIGTYTGPLQHGIVYSGGSSDTICDLLGAKGKDILYIGDHIFGDILKSKKRQGWRTFLVIPELAQELHVWTDKSSLFEELQSLD------------------------RRIKKVTHDMDMCYGMMGSLFRSGSRQTLFASQVMRYADLYAASFINLLYYPFSYLFRAAHVLMPHES 488
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392   |     -         -       422       432       442       452       462       472       482      
                                                                                                                                                                                                                                                                                                                                                                                                                                   396                      421                                                                   

   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  (0, 0)

(no "SCOP Domain" information available for 2XCV)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (1, 1)

Asymmetric Unit
(-)
Clan: HAD (186)

(-) Gene Ontology  (17, 17)

Asymmetric Unit(hide GO term definitions)
Chain A   (5NTC_HUMAN | P49902)
molecular function
    GO:0008253    5'-nucleotidase activity    Catalysis of the reaction: a 5'-ribonucleotide + H2O = a ribonucleoside + phosphate.
    GO:0003824    catalytic activity    Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
    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:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0050146    nucleoside phosphotransferase activity    Catalysis of the reaction: a nucleotide + a 2'-deoxynucleoside = a nucleoside + a 2'-deoxynucleoside 5'-monophosphate.
    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: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).
biological process
    GO:0046040    IMP metabolic process    The chemical reactions and pathways involving IMP, inosine monophosphate.
    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:0017144    drug metabolic process    The chemical reactions and pathways involving a drug, a substance used in the diagnosis, treatment or prevention of a disease; as used here antibiotic substances (see antibiotic metabolism) are considered to be drugs, even if not used in medical or veterinary practice.
    GO:0008152    metabolic process    The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation.
    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:0016310    phosphorylation    The process of introducing a phosphate group into a molecule, usually with the formation of a phosphoric ester, a phosphoric anhydride or a phosphoric amide.
    GO:0006195    purine nucleotide catabolic process    The chemical reactions and pathways resulting in the breakdown of a purine nucleotide, a compound consisting of nucleoside (a purine base linked to a deoxyribose or ribose sugar) esterified with a phosphate group at either the 3' or 5'-hydroxyl group of the sugar.
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.

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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        5NTC_HUMAN | P499022j2c 2jc9 2jcm 2xcw 2xcx 2xjb 2xjc 2xjd 2xje 2xjf 4h4b 5cqz 5cr7 5k7y 5l4z 5l50

(-) Related Entries Specified in the PDB File

2j2c CRYSTAL STRUCTURE OF HUMAN CYTOSOLIC 5'-NUCLEOTIDASE II (NT5C2, CN-II)
2jc9 CRYSTAL STRUCTURE OF HUMAN CYTOSOLIC 5'-NUCLEOTIDASE II IN COMPLEX WITH ADENOSINE
2jcm CRYSTAL STRUCTURE OF HUMAN CYTOSOLIC 5'-NUCLEOTIDASE II IN COMPLEX WITH BERYLLIUM TRIFLUORIDE
2xcw CRYSTAL STRUCTURE OF THE D52N VARIANT OF CYTOSOLIC 5 '-NUCLEOTIDASE II IN COMPLEX WITH INOSINE MONOPHOSPHATE AND ATP
2xcx CRYSTAL STRUCTURE OF THE APOFORM OF THE D52N VARIANT OF CYTOSOLIC 5'-NUCLEOTIDASE II
2xjb CRYSTAL STRUCTURE OF THE D52N VARIANT OF CYTOSOLIC 5 '-NUCLEOTIDASE II IN COMPLEX WITH DEOXYGUANOSINE MONOPHOSPHATE AND DEOXYADENOSINE TRIPHOSPHATE
2xjc CRYSTAL STRUCTURE OF THE D52N VARIANT OF CYTOSOLIC 5 '-NUCLEOTIDASE II IN COMPLEX WITH GUANOSINE MONOPHOSPHATE AND DIADENOSINE TETRAPHOSPHATE
2xjd CRYSTAL STRUCTURE OF THE D52N VARIANT OF CYTOSOLIC 5 '-NUCLEOTIDASE II IN COMPLEX WITH INORGANIC PHOSPHATE AND DEOXYADENOSINE TRIPHOSPHATE
2xje CRYSTAL STRUCTURE OF THE D52N VARIANT OF CYTOSOLIC 5 '-NUCLEOTIDASE II IN COMPLEX WITH URIDINE 5'- MONOPHOSPHATE AND ADENOSINE TRIPHOSPHATE
2xjf CRYSTAL STRUCTURE OF THE D52N VARIANT OF CYTOSOLIC 5 '-NUCLEOTIDASE II WITH A COVALENTLY MODIFIED ASN52