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(-) Description

Title :  MYCOBACTERIUM TUBERCULOSIS DUTPASE COMPLEXED WITH DUTP IN THE ABSENCE OF METAL ION.
 
Authors :  M. R. Sawaya, S. Chan, B. Segelke, T. Lekin, H. Krupka, U. S. Cho, M. -Y. Ki C. -Y. Kim, C. M. Naranjo, Y. C. Rogers, M. S. Park, G. S. Waldo, I. Pashko D. Cascio, T. O. Yeates, J. L. Perry, T. C. Terwilliger, D. Eisenberg, T Structural Genomics Consortium (Tbsgc)
Date :  09 Mar 04  (Deposition) - 16 Mar 04  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.10
Chains :  Asym./Biol. Unit :  A,B,C
Keywords :  Jelly-Roll, Structural Genomics, Psi, Protein Structure Initiative, Tb Structural Genomics Consortium, Tbsgc, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  S. Chan, B. Segelke, T. Lekin, H. Krupka, U. S. Cho, M. -Y. Kim, M. So, C. -Y. Kim, C. M. Naranjo, Y. C. Rogers, M. S. Park, G. S. Waldo, I. Pashkov, D. Cascio, J. L. Perry, M. R. Sawaya
Crystal Structure Of The Mycobacterium Tuberculosis Dutpase Insights Into The Catalytic Mechanism.
J. Mol. Biol. V. 341 503 2004
PubMed-ID: 15276840  |  Reference-DOI: 10.1016/J.JMB.2004.06.028

(-) Compounds

Molecule 1 - DEOXYURIDINE 5'-TRIPHOSPHATE NUCLEOTIDOHYDROLASE
    ChainsA, B, C
    EC Number3.6.1.23
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidMODIFIED PET28B
    Expression System StrainBL21PRO
    Expression System Taxid562
    Expression System Vector TypePLASMID
    GeneDUT, RV2697C, MT2771, MTCY05A6.18C, MB2716C
    Organism ScientificMYCOBACTERIUM TUBERCULOSIS
    Organism Taxid1773
    SynonymDUTPASE, DUTP PYROPHOSPHATASE

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit ABC

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 7)

Asymmetric/Biological Unit (3, 7)
No.NameCountTypeFull Name
1DUT3Ligand/IonDEOXYURIDINE-5'-TRIPHOSPHATE
2NO31Ligand/IonNITRATE ION
3TRS3Ligand/Ion2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREPHE A:130 , ASP A:131 , THR B:4 , ALA B:6 , ARG C:87 , VAL C:127BINDING SITE FOR RESIDUE NO3 C 155
2AC2SOFTWAREASN A:77 , GLY A:80 , THR A:81 , ILE A:82 , ASP A:83 , TYR A:86 , GLU A:89 , ILE A:90 , LYS A:91 , ARG B:140 , ARG C:64 , SER C:65 , GLY C:66 , GLN C:113 , HOH C:197 , HOH C:204 , HOH C:232 , HOH C:282 , HOH C:292 , HOH C:369BINDING SITE FOR RESIDUE DUT C 1170
3AC3SOFTWAREARG A:64 , SER A:65 , GLY A:66 , GLN A:113 , HOH A:182 , HOH A:222 , HOH A:269 , HOH A:314 , HOH A:364 , HOH A:365 , ASN B:77 , GLY B:80 , THR B:81 , ILE B:82 , ASP B:83 , TYR B:86 , GLU B:89 , ILE B:90 , LYS B:91 , HOH B:251BINDING SITE FOR RESIDUE DUT A 2170
4AC4SOFTWAREASP B:28 , PRO B:63 , ARG B:64 , SER B:65 , GLY B:66 , GLN B:113 , HOH B:306 , ASN C:77 , GLY C:80 , THR C:81 , ILE C:82 , ASP C:83 , TYR C:86 , GLU C:89 , ILE C:90 , LYS C:91 , HOH C:169 , HOH C:241 , HOH C:275BINDING SITE FOR RESIDUE DUT C 3170
5AC5SOFTWARESER A:74 , ILE A:75 , VAL A:76 , SER B:74 , ILE B:75 , SER C:74 , ILE C:75 , VAL C:76 , LEU C:97 , HOH C:181 , HOH C:191 , HOH C:198BINDING SITE FOR RESIDUE TRS C 3171
6AC6SOFTWARELEU A:60 , HIS A:62 , PRO A:79 , GLN A:117 , LEU B:60 , HIS B:62 , GLN B:117 , LEU C:60 , HIS C:62 , PRO C:79 , GLN C:117BINDING SITE FOR RESIDUE TRS A 2171
7AC7SOFTWAREGLY A:40 , LEU B:97 , HOH B:236 , HOH B:301 , HOH B:344 , GLY C:40 , ASN C:96BINDING SITE FOR RESIDUE TRS B 155

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1SMC)

(-) Cis Peptide Bonds  (3, 3)

Asymmetric/Biological Unit
No.Residues
1Ser A:78 -Pro A:79
2Ser B:78 -Pro B:79
3Ser C:78 -Pro C:79

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1SMC)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1SMC)

(-) Exons   (0, 0)

(no "Exon" information available for 1SMC)

(-) 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:131
 aligned with DUT_MYCTO | P9WNS4 from UniProtKB/Swiss-Prot  Length:154

    Alignment length:131
                                    11        21        31        41        51        61        71        81        91       101       111       121       131 
            DUT_MYCTO     2 STTLAIVRLDPGLPLPSRAHDGDAGVDLYSAEDVELAPGRRALVRTGVAVAVPFGMVGLVHPRSGLATRVGLSIVNSPGTIDAGYRGEIKVALINLDPAAPIVVHRGDRIAQLLVQRVELVELVEVSSFDE 132
               SCOP domains d1smca_ A: Deoxyuridine 5'-triphosphate nucleotidohydrolase (dUTPase)                                                               SCOP domains
               CATH domains 1smcA00 A:2-132  [code=2.70.40.10, no name defined]                                                                                 CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee..................eeee....eee....eeeee...eee....eeeeee.hhhhhhhhheee....eeee.......eeeeee......eee....eeeeeeeee....eeee...... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1smc A   2 STTLAIVRLDPGLPLPSRAHDGDAGVDLYSAEDVELAPGRRALVRTGVAVAVPFGMVGLVHPRSGLATRVGLSIVNSPGTIDAGYRGEIKVALINLDPAAPIVVHRGDRIAQLLVQRVELVELVEVSSFDE 132
                                    11        21        31        41        51        61        71        81        91       101       111       121       131 

Chain A from PDB  Type:PROTEIN  Length:131
 aligned with DUT_MYCTU | P9WNS5 from UniProtKB/Swiss-Prot  Length:154

    Alignment length:131
                                    11        21        31        41        51        61        71        81        91       101       111       121       131 
            DUT_MYCTU     2 STTLAIVRLDPGLPLPSRAHDGDAGVDLYSAEDVELAPGRRALVRTGVAVAVPFGMVGLVHPRSGLATRVGLSIVNSPGTIDAGYRGEIKVALINLDPAAPIVVHRGDRIAQLLVQRVELVELVEVSSFDE 132
               SCOP domains d1smca_ A: Deoxyuridine 5'-triphosphate nucleotidohydrolase (dUTPase)                                                               SCOP domains
               CATH domains 1smcA00 A:2-132  [code=2.70.40.10, no name defined]                                                                                 CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee..................eeee....eee....eeeee...eee....eeeeee.hhhhhhhhheee....eeee.......eeeeee......eee....eeeeeeeee....eeee...... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1smc A   2 STTLAIVRLDPGLPLPSRAHDGDAGVDLYSAEDVELAPGRRALVRTGVAVAVPFGMVGLVHPRSGLATRVGLSIVNSPGTIDAGYRGEIKVALINLDPAAPIVVHRGDRIAQLLVQRVELVELVEVSSFDE 132
                                    11        21        31        41        51        61        71        81        91       101       111       121       131 

Chain B from PDB  Type:PROTEIN  Length:138
 aligned with DUT_MYCTO | P9WNS4 from UniProtKB/Swiss-Prot  Length:154

    Alignment length:141
                             1                                                                                                                                           
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139 
            DUT_MYCTO     - -MSTTLAIVRLDPGLPLPSRAHDGDAGVDLYSAEDVELAPGRRALVRTGVAVAVPFGMVGLVHPRSGLATRVGLSIVNSPGTIDAGYRGEIKVALINLDPAAPIVVHRGDRIAQLLVQRVELVELVEVSSFDEAGLASTSR 140
               SCOP domains d1smcb_ B: Deoxyuridine 5'-triphosphate nucleotidohydrolase (dUTPase)                                                                         SCOP domains
               CATH domains 1smcB00 B:0-140  [code=2.70.40.10, no name defined]                                                                                           CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeee.................eeee....eee....eeeee..eeee....eeeeee.hhhhhhhhheee....eee........eeeeee......eee....eeeeeeeee....eeee..hhhhhh..---. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1smc B   0 HMSTTLAIVRLDPGLPLPSRAHDGDAGVDLYSAEDVELAPGRRALVRTGVAVAVPFGMVGLVHPRSGLATRVGLSIVNSPGTIDAGYRGEIKVALINLDPAAPIVVHRGDRIAQLLVQRVELVELVEVSSFDEAGLA---R 140
                                     9        19        29        39        49        59        69        79        89        99       109       119       129      |  -|
                                                                                                                                                                  136 140

Chain B from PDB  Type:PROTEIN  Length:138
 aligned with DUT_MYCTU | P9WNS5 from UniProtKB/Swiss-Prot  Length:154

    Alignment length:141
                             1                                                                                                                                           
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139 
            DUT_MYCTU     - -MSTTLAIVRLDPGLPLPSRAHDGDAGVDLYSAEDVELAPGRRALVRTGVAVAVPFGMVGLVHPRSGLATRVGLSIVNSPGTIDAGYRGEIKVALINLDPAAPIVVHRGDRIAQLLVQRVELVELVEVSSFDEAGLASTSR 140
               SCOP domains d1smcb_ B: Deoxyuridine 5'-triphosphate nucleotidohydrolase (dUTPase)                                                                         SCOP domains
               CATH domains 1smcB00 B:0-140  [code=2.70.40.10, no name defined]                                                                                           CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeee.................eeee....eee....eeeee..eeee....eeeeee.hhhhhhhhheee....eee........eeeeee......eee....eeeeeeeee....eeee..hhhhhh..---. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1smc B   0 HMSTTLAIVRLDPGLPLPSRAHDGDAGVDLYSAEDVELAPGRRALVRTGVAVAVPFGMVGLVHPRSGLATRVGLSIVNSPGTIDAGYRGEIKVALINLDPAAPIVVHRGDRIAQLLVQRVELVELVEVSSFDEAGLA---R 140
                                     9        19        29        39        49        59        69        79        89        99       109       119       129      |  -|
                                                                                                                                                                  136 140

Chain C from PDB  Type:PROTEIN  Length:129
 aligned with DUT_MYCTO | P9WNS4 from UniProtKB/Swiss-Prot  Length:154

    Alignment length:129
                                    11        21        31        41        51        61        71        81        91       101       111       121         
            DUT_MYCTO     2 STTLAIVRLDPGLPLPSRAHDGDAGVDLYSAEDVELAPGRRALVRTGVAVAVPFGMVGLVHPRSGLATRVGLSIVNSPGTIDAGYRGEIKVALINLDPAAPIVVHRGDRIAQLLVQRVELVELVEVSSF 130
               SCOP domains d1smcc_ C: Deoxyuridine 5'-triphosphate nucleotidohydrolase (dUTPase)                                                             SCOP domains
               CATH domains 1smcC00 C:2-130  [code=2.70.40.10, no name defined]                                                                               CATH domains
           Pfam domains (1) ------------dUTPase-1smcC01 C:14-130                                                                                              Pfam domains (1)
           Pfam domains (2) ------------dUTPase-1smcC02 C:14-130                                                                                              Pfam domains (2)
           Pfam domains (3) ------------dUTPase-1smcC03 C:14-130                                                                                              Pfam domains (3)
         Sec.struct. author ..eeeeee.................eeee....eee....eeeeeeeeeee....eeeeee.hhhhhhhhheee....eee......eeeeeeee......eee....eeeeeeeee....eeee.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1smc C   2 STTLAIVRLDPGLPLPSRAHDGDAGVDLYSAEDVELAPGRRALVRTGVAVAVPFGMVGLVHPRSGLATRVGLSIVNSPGTIDAGYRGEIKVALINLDPAAPIVVHRGDRIAQLLVQRVELVELVEVSSF 130
                                    11        21        31        41        51        61        71        81        91       101       111       121         

Chain C from PDB  Type:PROTEIN  Length:129
 aligned with DUT_MYCTU | P9WNS5 from UniProtKB/Swiss-Prot  Length:154

    Alignment length:129
                                    11        21        31        41        51        61        71        81        91       101       111       121         
            DUT_MYCTU     2 STTLAIVRLDPGLPLPSRAHDGDAGVDLYSAEDVELAPGRRALVRTGVAVAVPFGMVGLVHPRSGLATRVGLSIVNSPGTIDAGYRGEIKVALINLDPAAPIVVHRGDRIAQLLVQRVELVELVEVSSF 130
               SCOP domains d1smcc_ C: Deoxyuridine 5'-triphosphate nucleotidohydrolase (dUTPase)                                                             SCOP domains
               CATH domains 1smcC00 C:2-130  [code=2.70.40.10, no name defined]                                                                               CATH domains
           Pfam domains (1) ------------dUTPase-1smcC01 C:14-130                                                                                              Pfam domains (1)
           Pfam domains (2) ------------dUTPase-1smcC02 C:14-130                                                                                              Pfam domains (2)
           Pfam domains (3) ------------dUTPase-1smcC03 C:14-130                                                                                              Pfam domains (3)
         Sec.struct. author ..eeeeee.................eeee....eee....eeeeeeeeeee....eeeeee.hhhhhhhhheee....eee......eeeeeeee......eee....eeeeeeeee....eeee.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1smc C   2 STTLAIVRLDPGLPLPSRAHDGDAGVDLYSAEDVELAPGRRALVRTGVAVAVPFGMVGLVHPRSGLATRVGLSIVNSPGTIDAGYRGEIKVALINLDPAAPIVVHRGDRIAQLLVQRVELVELVEVSSF 130
                                    11        21        31        41        51        61        71        81        91       101       111       121         

   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, 3)

Asymmetric/Biological Unit

(-) CATH Domains  (1, 3)

Asymmetric/Biological Unit
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (1, 3)

Asymmetric/Biological Unit
(-)
Clan: dUTPase (38)

(-) Gene Ontology  (11, 19)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B,C   (DUT_MYCTO | P9WNS4)
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: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.
biological process
    GO:0006226    dUMP biosynthetic process    The chemical reactions and pathways resulting in the formation of dUMP, deoxyuridine monophosphate (2'-deoxyuridine 5'-phosphate).
    GO:0046080    dUTP metabolic process    The chemical reactions and pathways involving dUTP, deoxyuridine (5'-)triphosphate.
    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:0006220    pyrimidine nucleotide metabolic process    The chemical reactions and pathways involving a pyrimidine nucleotide, a compound consisting of nucleoside (a pyrimidine base linked to a deoxyribose or ribose sugar) esterified with a phosphate group at either the 3' or 5'-hydroxyl group of the sugar.

Chain A,B,C   (DUT_MYCTU | P9WNS5)
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: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.
biological process
    GO:0006226    dUMP biosynthetic process    The chemical reactions and pathways resulting in the formation of dUMP, deoxyuridine monophosphate (2'-deoxyuridine 5'-phosphate).
    GO:0046081    dUTP catabolic process    The chemical reactions and pathways resulting in the breakdown of dUTP, deoxyuridine (5'-)triphosphate.
    GO:0046080    dUTP metabolic process    The chemical reactions and pathways involving dUTP, deoxyuridine (5'-)triphosphate.
    GO:0040007    growth    The increase in size or mass of an entire organism, a part of an organism or a cell.
    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:0006220    pyrimidine nucleotide metabolic process    The chemical reactions and pathways involving a pyrimidine nucleotide, a compound consisting of nucleoside (a pyrimidine 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.

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 Related Entries

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

UniProtKB/Swiss-Prot
        DUT_MYCTO | P9WNS41mq7 1six 1sjn 1slh 1sm8 1snf 2py4 3h6d 3hza 3i93 3loj 4gcy
        DUT_MYCTU | P9WNS51mq7 1six 1sjn 1slh 1sm8 1snf 2py4 3h6d 3hza 3i93 3loj 4gcy 5ect 5edd

(-) Related Entries Specified in the PDB File

1mq7 M.TUBERCULOSIS DUTPASE UNLIGANDED
1six M.TUBERCULOSIS DUTPASE COMPLEXED WITH MAGNESIUM AND ALPHA, BETA-IMIDO-DUTP
1sjn M.TUBERCULOSIS DUTPASE COMPLEXED WITH MAGNESIUM AND ALPHA, BETA-IMIDO-DUTP
1slh M.TUBERCULOSIS DUTPASE COMPLEXED WITH MAGNESIUM AND DUDP
1sm8 M.TUBERCULOSIS DUTPASE COMPLEXED WITH CHROMIUM AND DUTP RELATED ID: RV2697C RELATED DB: TARGETDB