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(-) Description

Title :  THE CRYSTAL STRUCTURE OF LEISHMANIA MAJOR DUTPASE IN COMPLEX DUMP
 
Authors :  G. R. Hemsworth, O. V. Moroz, M. J. Fogg, B. Scott, C. Bosch-Navarrete, D. Gonzalez-Pacanowska, K. S. Wilson
Date :  25 Feb 11  (Deposition) - 16 Mar 11  (Release) - 11 May 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.40
Chains :  Asym. Unit :  A,B,D,E
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  D,E  (1x)
Keywords :  Hydrolase, Leishmaniasis (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  G. R. Hemsworth, O. V. Moroz, M. J. Fogg, B. Scott, C. Bosch-Navarrete, D. Gonzalez-Pacanowska, K. S. Wilson
The Crystal Structure Of The Leishmania Major Deoxyuridine Triphosphate Nucleotidohydrolase In Complex With Nucleotide Analogues, Dump, And Deoxyuridine.
J. Biol. Chem. V. 286 16470 2011
PubMed-ID: 21454646  |  Reference-DOI: 10.1074/JBC.M111.224873

(-) Compounds

Molecule 1 - DUTPASE
    ChainsA, B, D, E
    EC Number3.6.1.23
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET-YSBLLIC3C
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    Expression System Vector TypePLASMID
    Organism ScientificLEISHMANIA MAJOR
    Organism Taxid5664
    Strain252
    SynonymDEOXYURIDINE TRIPHOSPHATASE (DUTP DIPHOSPHATASE), DEOXYURIDINE TRIPHOSPHATE NUCLEOTIDOHYDROLASE

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit ABDE
Biological Unit 1 (1x)AB  
Biological Unit 2 (1x)  DE

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 11)

Asymmetric Unit (3, 11)
No.NameCountTypeFull Name
1MG3Ligand/IonMAGNESIUM ION
2SO44Ligand/IonSULFATE ION
3UMP4Ligand/Ion2'-DEOXYURIDINE 5'-MONOPHOSPHATE
Biological Unit 1 (2, 4)
No.NameCountTypeFull Name
1MG-1Ligand/IonMAGNESIUM ION
2SO42Ligand/IonSULFATE ION
3UMP2Ligand/Ion2'-DEOXYURIDINE 5'-MONOPHOSPHATE
Biological Unit 2 (2, 4)
No.NameCountTypeFull Name
1MG-1Ligand/IonMAGNESIUM ION
2SO42Ligand/IonSULFATE ION
3UMP2Ligand/Ion2'-DEOXYURIDINE 5'-MONOPHOSPHATE

(-) Sites  (11, 11)

Asymmetric Unit (11, 11)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREGLN A:21 , LEU A:24 , ASN A:25 , ILE A:28 , TRP A:41 , ASP A:79 , HIS A:82 , PHE A:83 , ASN A:183 , ARG A:186 , TYR A:191 , LYS A:198 , LYS B:59 , TRP B:60 , TRP B:61BINDING SITE FOR RESIDUE UMP A1265
02AC2SOFTWAREVAL A:197 , LYS A:198 , VAL A:199 , LYS B:62BINDING SITE FOR RESIDUE SO4 A1266
03AC3SOFTWAREGLU A:48 , GLU A:76 , ASP A:79BINDING SITE FOR RESIDUE MG A1267
04AC4SOFTWARELYS A:59 , LYS A:62 , ASN A:63BINDING SITE FOR RESIDUE SO4 A1268
05AC5SOFTWARETRP A:60 , TRP A:61 , GLN B:21 , LEU B:24 , ASN B:25 , ILE B:28 , TRP B:41 , GLU B:48 , ASP B:79 , HIS B:82 , PHE B:83 , LYS B:179 , ASN B:183 , ARG B:186 , TYR B:191 , HOH B:2006BINDING SITE FOR RESIDUE UMP B1265
06AC6SOFTWAREGLN D:21 , LEU D:24 , ASN D:25 , ILE D:28 , TRP D:41 , ASP D:79 , HIS D:82 , PHE D:83 , ASN D:183 , ARG D:186 , TYR D:191 , MG D:1266 , LYS E:59 , TRP E:60 , TRP E:61BINDING SITE FOR RESIDUE UMP D1265
07AC7SOFTWAREGLU D:48 , GLU D:76 , ASP D:79 , LYS D:179 , UMP D:1265BINDING SITE FOR RESIDUE MG D1266
08AC8SOFTWARELYS D:59 , LYS D:62 , ASN D:63BINDING SITE FOR RESIDUE SO4 D1267
09AC9SOFTWARELYS E:59 , LYS E:62 , ASN E:63BINDING SITE FOR RESIDUE SO4 E1265
10BC1SOFTWARETRP D:60 , TRP D:61 , GLN E:21 , LEU E:24 , ASN E:25 , ILE E:28 , TRP E:41 , GLU E:48 , ASP E:79 , HIS E:82 , PHE E:83 , LYS E:179 , ASN E:183 , ARG E:186 , TYR E:191 , MG E:1267 , HOH E:2004BINDING SITE FOR RESIDUE UMP E1266
11BC2SOFTWAREGLU E:48 , GLU E:76 , ASP E:79 , UMP E:1266BINDING SITE FOR RESIDUE MG E1267

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (4, 4)

Asymmetric Unit
No.Residues
1Phe A:130 -Pro A:131
2Phe B:130 -Pro B:131
3Phe D:130 -Pro D:131
4Phe E:130 -Pro E:131

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 2YAZ)

(-) 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:257
 aligned with O15826_LEIMA | O15826 from UniProtKB/TrEMBL  Length:268

    Alignment length:257
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       
         O15826_LEIMA     8 NIPGAILHSLAELQDGLNAMIDPSWRAVRSLDNWALAITMESTELLDSYPWKWWKNLNATPDLANVRIELVDIFHFSLSGAMQMRSTPDDEIPAASLKPLKEVMTTFLPAKECTSDPYGFVFFPLTDTQNAIASFRNIIQLANAYRFDVIIECIIYAAEDLGFNLVAYYIAKHTLNCIRQLSGYKDGSYVKVNNGVEDNSLLHNCIKDVSLDEVLDADKYVQAWNSIMANVYEAFQIKESDRKDAERWFALAKENRL 264
               SCOP domains d2yaza_ A: automated matches                                                                                                                                                                                                                                      SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhh..............hhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhh.........ee......ee...hhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhh.........ee..ee.hhhhhhhhh..hhhhhhh..hhhhhhhhhhhhhhhhh..hhhhh.hhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2yaz A   8 NIPGAILHSLAELQDGLNAMIDPSWRAVRSLDNWALAITMESTELLDSYPWKWWKNLNATPDLANVRIELVDIFHFSLSGAMQMRSTPDDEIPAASLKPLKEVMTTFLPAKECTSDPYGFVFFPLTDTQNAIASFRNIIQLANAYRFDVIIECIIYAAEDLGFNLVAYYIAKHTLNCIRQLSGYKDGSYVKVNNGVEDNSLLHNCIKDVSLDEVLDADKYVQAWNSIMANVYEAFQIKESDRKDAERWFALAKENRL 264
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       

Chain B from PDB  Type:PROTEIN  Length:263
 aligned with O15826_LEIMA | O15826 from UniProtKB/TrEMBL  Length:268

    Alignment length:263
                                    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   
         O15826_LEIMA     2 KRARSANIPGAILHSLAELQDGLNAMIDPSWRAVRSLDNWALAITMESTELLDSYPWKWWKNLNATPDLANVRIELVDIFHFSLSGAMQMRSTPDDEIPAASLKPLKEVMTTFLPAKECTSDPYGFVFFPLTDTQNAIASFRNIIQLANAYRFDVIIECIIYAAEDLGFNLVAYYIAKHTLNCIRQLSGYKDGSYVKVNNGVEDNSLLHNCIKDVSLDEVLDADKYVQAWNSIMANVYEAFQIKESDRKDAERWFALAKENRL 264
               SCOP domains d2yazb_ B: automated matches                                                                                                                                                                                                                                            SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........hhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhh..............hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhh..........ee......ee...hhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhh..............hhhhhhhhh.............hhhhhhhhhhhhhhhhh..hhhhh.hhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2yaz B   2 KRARSANIPGAILHSLAELQDGLNAMIDPSWRAVRSLDNWALAITMESTELLDSYPWKWWKNLNATPDLANVRIELVDIFHFSLSGAMQMRSTPDDEIPAASLKPLKEVMTTFLPAKECTSDPYGFVFFPLTDTQNAIASFRNIIQLANAYRFDVIIECIIYAAEDLGFNLVAYYIAKHTLNCIRQLSGYKDGSYVKVNNGVEDNSLLHNCIKDVSLDEVLDADKYVQAWNSIMANVYEAFQIKESDRKDAERWFALAKENRL 264
                                    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   

Chain D from PDB  Type:PROTEIN  Length:257
 aligned with O15826_LEIMA | O15826 from UniProtKB/TrEMBL  Length:268

    Alignment length:257
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       
         O15826_LEIMA     8 NIPGAILHSLAELQDGLNAMIDPSWRAVRSLDNWALAITMESTELLDSYPWKWWKNLNATPDLANVRIELVDIFHFSLSGAMQMRSTPDDEIPAASLKPLKEVMTTFLPAKECTSDPYGFVFFPLTDTQNAIASFRNIIQLANAYRFDVIIECIIYAAEDLGFNLVAYYIAKHTLNCIRQLSGYKDGSYVKVNNGVEDNSLLHNCIKDVSLDEVLDADKYVQAWNSIMANVYEAFQIKESDRKDAERWFALAKENRL 264
               SCOP domains d2yazd_ D: automated matches                                                                                                                                                                                                                                      SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhh..............hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..........ee......ee...hhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhh.........ee..ee...hhhhhhhhh.........hhhhhhhhhhhhhhhhh..hhhhh.hhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2yaz D   8 NIPGAILHSLAELQDGLNAMIDPSWRAVRSLDNWALAITMESTELLDSYPWKWWKNLNATPDLANVRIELVDIFHFSLSGAMQMRSTPDDEIPAASLKPLKEVMTTFLPAKECTSDPYGFVFFPLTDTQNAIASFRNIIQLANAYRFDVIIECIIYAAEDLGFNLVAYYIAKHTLNCIRQLSGYKDGSYVKVNNGVEDNSLLHNCIKDVSLDEVLDADKYVQAWNSIMANVYEAFQIKESDRKDAERWFALAKENRL 264
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       

Chain E from PDB  Type:PROTEIN  Length:257
 aligned with O15826_LEIMA | O15826 from UniProtKB/TrEMBL  Length:268

    Alignment length:257
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       
         O15826_LEIMA     8 NIPGAILHSLAELQDGLNAMIDPSWRAVRSLDNWALAITMESTELLDSYPWKWWKNLNATPDLANVRIELVDIFHFSLSGAMQMRSTPDDEIPAASLKPLKEVMTTFLPAKECTSDPYGFVFFPLTDTQNAIASFRNIIQLANAYRFDVIIECIIYAAEDLGFNLVAYYIAKHTLNCIRQLSGYKDGSYVKVNNGVEDNSLLHNCIKDVSLDEVLDADKYVQAWNSIMANVYEAFQIKESDRKDAERWFALAKENRL 264
               SCOP domains d2yaze_ E: automated matches                                                                                                                                                                                                                                      SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) -----dUTPase_2-2yazE01 E:13-191                                                                                                                                                         ------------------------------------------------------------------------- Pfam domains (1)
           Pfam domains (2) -----dUTPase_2-2yazE02 E:13-191                                                                                                                                                         ------------------------------------------------------------------------- Pfam domains (2)
           Pfam domains (3) -----dUTPase_2-2yazE03 E:13-191                                                                                                                                                         ------------------------------------------------------------------------- Pfam domains (3)
           Pfam domains (4) -----dUTPase_2-2yazE04 E:13-191                                                                                                                                                         ------------------------------------------------------------------------- Pfam domains (4)
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhh..............hhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhh.........ee......ee...hhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhh.........ee..ee.hhhhhhhhh...hhhhh...hhhhhhhhhhhhhhhhh..hhhhh.hhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2yaz E   8 NIPGAILHSLAELQDGLNAMIDPSWRAVRSLDNWALAITMESTELLDSYPWKWWKNLNATPDLANVRIELVDIFHFSLSGAMQMRSTPDDEIPAASLKPLKEVMTTFLPAKECTSDPYGFVFFPLTDTQNAIASFRNIIQLANAYRFDVIIECIIYAAEDLGFNLVAYYIAKHTLNCIRQLSGYKDGSYVKVNNGVEDNSLLHNCIKDVSLDEVLDADKYVQAWNSIMANVYEAFQIKESDRKDAERWFALAKENRL 264
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       

   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, 4)

Asymmetric Unit

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (1, 4)

Asymmetric Unit
(-)
Clan: MazG (25)

(-) Gene Ontology  (3, 3)

Asymmetric Unit(hide GO term definitions)
Chain A,B,D,E   (O15826_LEIMA | O15826)
molecular function
    GO:0004170    dUTP diphosphatase activity    Catalysis of the reaction: dUTP + H2O = dUMP + diphosphate.
    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.

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 Related Entries

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

UniProtKB/TrEMBL
        O15826_LEIMA | O158262cje 2yay 2yb0

(-) Related Entries Specified in the PDB File

2cic THE CRYSTAL STRUCTURE OF A COMPLEX OF CAMPYLOBACTER JEJUNI DUTPASE WITH SUBSTRATE ANALOGUE DUPNHPP
2cje THE CRYSTAL STRUCTURE OF A COMPLEX OF LEISHMANIA MAJOR DUTPASE WITH SUBSTRATE ANALOGUE DUPNHP
2yay THE CRYSTAL STRUCTURE OF LEISHMANIA MAJOR DUTPASE IN COMPLEX WITH SUBSTRATE ANALOGUE DUPNPP
2yb0 THE CRYSTAL STRUCTURE OF LEISHMANIA MAJOR DUTPASE IN COMPLEX DEOXYURIDINE