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(-) Description

Title :  CRYSTAL STRUCTURE OF AN ALPHA-KETOGLUTARATE-DEPENDENT TAURINE DIOXYGENASE FROM MYCOBACTERIUM SMEGMATIS
 
Authors :  Seattle Structural Genomics Center For Infectious Disease (S
Date :  08 Feb 13  (Deposition) - 20 Feb 13  (Release) - 22 Apr 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.60
Chains :  Asym. Unit :  A,B,C,D,E,F,G,H
Biol. Unit 1:  A,B,C,D  (1x)
Biol. Unit 2:  E,F,G,H  (1x)
Keywords :  Structural Genomics, Niaid, National Institute Of Allergy And Infectious Diseases, Seattle Structural Genomics Center For Infectious Disease, Ssgcid, Taud, Oxidoreductase, Iron-Dependent, Molecular Oxygen (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  L. Baugh, I. Phan, D. W. Begley, M. C. Clifton, B. Armour, D. M. Dranow, B. M. Taylor, M. M. Muruthi, J. Abendroth, J. W. Fairman, D. Fox, S. H. Dieterich, B. L. Staker, A. S. Gardberg, R. Choi, S. N. Hewitt, A. J. Napuli, J. Myers, L. K. Barrett, Y. Zhang, M. Ferrell, E. Mundt, K. Thompkins, N. Tran, S. Lyons-Abbott, A. Abramov, A. Sekar, D. Serbzhinskiy, D. Lorimer, G. W. Buchko, R. Stacy, L. J. Stewart, T. E. Edwards, W. C. Van Voorhis, P. J. Myler
Increasing The Structural Coverage Of Tuberculosis Drug Targets.
Tuberculosis (Edinb) V. 95 142 2015
PubMed-ID: 25613812  |  Reference-DOI: 10.1016/J.TUBE.2014.12.003

(-) Compounds

Molecule 1 - ALPHA-KETOGLUTARATE-DEPENDENT TAURINE DIOXYGENASE
    Chains: A, B, C, D, E, F, G, H
    EC Number: 1.14.11.17
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Expression System Vector Type: PAVA0421
    Gene: MSMEG_3870
    Organism Scientific: MYCOBACTERIUM SMEGMATIS
    Organism Taxid: 246196
    Strain: ATCC 700084

 Structural Features

(-) Chains, Units

  12345678
Asymmetric Unit : ABCDEFGH
Biological Unit 1 (1x): ABCD    
Biological Unit 2 (1x):     EFGH

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 10)

Asymmetric Unit (3, 10)
No.NameCountTypeFull Name
1EDO1Ligand/Ion1,2-ETHANEDIOL
2FE8Ligand/IonFE (III) ION
3MG1Ligand/IonMAGNESIUM ION
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1EDO1Ligand/Ion1,2-ETHANEDIOL
2FE-1Ligand/IonFE (III) ION
3MG-1Ligand/IonMAGNESIUM ION
Biological Unit 2 (0, 0)
No.NameCountTypeFull Name
1EDO-1Ligand/Ion1,2-ETHANEDIOL
2FE-1Ligand/IonFE (III) ION
3MG-1Ligand/IonMAGNESIUM ION

(-) Sites  (10, 10)

Asymmetric Unit (10, 10)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREHIS A:95 , ASP A:97 , HIS A:248 , HOH A:532BINDING SITE FOR RESIDUE FE A 401
02AC2SOFTWAREASP A:220 , ARG A:221 , ARG A:224 , HOH B:509BINDING SITE FOR RESIDUE EDO A 402
03AC3SOFTWAREHIS B:95 , ASP B:97 , HIS B:248 , ARG B:263 , HOH B:580BINDING SITE FOR RESIDUE FE B 401
04AC4SOFTWAREHIS C:95 , ASP C:97 , HIS C:248 , ARG C:263BINDING SITE FOR RESIDUE FE C 401
05AC5SOFTWAREHIS D:95 , ASP D:97 , HIS D:248 , ARG D:263BINDING SITE FOR RESIDUE FE D 401
06AC6SOFTWAREHIS E:95 , ASP E:97 , HIS E:248 , ARG E:263 , HOH E:564BINDING SITE FOR RESIDUE FE E 401
07AC7SOFTWAREHIS F:95 , ASP F:97 , HIS F:248 , ARG F:263 , HOH F:561BINDING SITE FOR RESIDUE FE F 401
08AC8SOFTWAREGLU F:62 , GLY F:65 , HOH F:538 , HOH F:539BINDING SITE FOR RESIDUE MG F 402
09AC9SOFTWAREHIS G:95 , ASP G:97 , HIS G:248 , ARG G:263BINDING SITE FOR RESIDUE FE G 401
10BC1SOFTWAREHIS H:95 , ASP H:97 , HIS H:248 , ARG H:263 , HOH H:553 , HOH H:554BINDING SITE FOR RESIDUE FE H 401

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4J5I)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4J5I)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4J5I)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4J5I)

(-) Exons   (0, 0)

(no "Exon" information available for 4J5I)

(-) 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:248
                                                                                                                                                                                                                                                                                        
               SCOP domains d4j5ia_ A: automated matches                                                                                                                                                                                                                             SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee......eeee........hhhhhhhhhhhhhhhheeee......hhhhhhhhhhhhh....................eeeeeeee.......eeeeehhhhhhh.hhhhhhhhhhheeeee.....eeeee.eee......eee.....eeee...hhhhhhhhhhhhhhhhhh...eeee......eeeee...eeeee.........eeeeeee.............eeee......... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4j5i A   3 QVTVTKLGAHIGARIDGVRVGGDLSPATVSAINAALLEHKVIFFSGQDHLDDAGQLEFAELLGTPTVANSWHTDVTFVDRIPKASLLRAVTLPSYGGTTAWASTEAAYQQLPAPLRTLADNLWAVHTNRDYYEVEHPVVRVHPETGERVLLLGHFVKSFVGLKDTESAALFRLFQDRITRLENTVRWSWKPGDLAIWDNRATQHYAVADYDDQYRRLNRVTLAGDIPVDVYGERSRVIAGDASSYSPV 292
                                    12        22        32        42        52        62      ||93       103       113       123       133       143       174       184       194       204       214       224       234       244       254       264       274       284        
                                                                                             69|                                                          152|                                                                                                                      
                                                                                              91                                                           174                                                                                                                      


Chain B from PDB  Type:PROTEIN  Length:285
                                                                                                                                                                                                                                                                                                                             
               SCOP domains d4j5ib_ B: automated matches                                                                                                                                                                                                                                                                  SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee......eeee........hhhhhhhhhhhhhhhheeee......hhhhhhhhhhhhh...............eeeee.....................eeeeeeee.......eeeeehhhhhhh.hhhhhhhhhhheeeee...hhhhhhhhhhhh....eeeee.eee......eee.....eeee...hhhhhhhhhhhhhhhhhh...eeee......eeeee...eeeee.........eeeeeee.............eeee.......... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4j5i B   2 VQVTVTKLGAHIGARIDGVRVGGDLSPATVSAINAALLEHKVIFFSGQDHLDDAGQLEFAELLGTPTVAHPTLAEGAEQLLPIDSRYDKANSWHTDVTFVDRIPKASLLRAVTLPSYGGTTAWASTEAAYQQLPAPLRTLADNLWAVHTNRISAEQRGYRQRFESDYYEVEHPVVRVHPETGERVLLLGHFVKSFVGLKDTESAALFRLFQDRITRLENTVRWSWKPGDLAIWDNRATQHYAVADYDDQYRRLNRVTLAGDIPVDVYGERSRVIAGDASSYSPVD 293
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151||     168       178       188       198       208       218       228       238       248       258       268       278       288     
                                                                                                                                                                                152|                                                                                                                                     
                                                                                                                                                                                 160                                                                                                                                     


Chain C from PDB  Type:PROTEIN  Length:271
                                                                                                                                                                                                                                                                                                               
               SCOP domains d4j5ic_ C: automated matches                                                                                                                                                                                                                                                    SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee......eeee........hhhhhhhhhhhhhhhheeee......hhhhhhhhhhhhh...............eeeee.....................eeeeeeee.......eeeeehhhhhhh.hhhhhhhhhhheeeee.....eeeee.eee......eee.....eeee...hhhhhhhhhhhhhhhhhh...eeee......eeeee...eeeee.........eeeeeee.............eeee.......... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4j5i C   2 VQVTVTKLGAHIGARIDGVRVGGDLSPATVSAINAALLEHKVIFFSGQDHLDDAGQLEFAELLGTPTVAHPTLAEGAEQLLPIDSRYDKANSWHTDVTFVDRIPKASLLRAVTLPSYGGTTAWASTEAAYQQLPAPLRTLADNLWAVHTNRDYYEVEHPVVRVHPETGERVLLLGHFVKSFVGLKDTESAALFRLFQDRITRLENTVRWSWKPGDLAIWDNRATQHYAVADYDDQYRRLNRVTLAGDIPVDVYGERSRVIAGDASSYSPVD 293
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151||     182       192       202       212       222       232       242       252       262       272       282       292 
                                                                                                                                                                                152|                                                                                                                       
                                                                                                                                                                                 174                                                                                                                       


Chain D from PDB  Type:PROTEIN  Length:239
                                                                                                                                                                                                                                                                               
               SCOP domains d4j5id_ D: automated matches                                                                                                                                                                                                                    SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee......eeee........hhhhhhhhhhhhhhhheeee......hhhhhhhhhhhhh...................eeeeeeee.......eeeeehhhhhhh.hhhhhhhhhhheeeee.....eeeee.eee......eee.....eeee...hhhhhhhhhhhhhhhhhh...eeee......eeeee...eeeee.........eeeeeee.............eeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4j5i D   3 QVTVTKLGAHIGARIDGVRVGGDLSPATVSAINAALLEHKVIFFSGQDHLDDAGQLEFAELLGTPTANSWHTDVTFVDRIPKASLLRAVTLPSYGGTTAWASTEAAYQQLPAPLRTLADNLWAVHTNRDYYEVEHPVVRVHPETGERVLLLGHFVKSFVGLKDTESAALFRLFQDRITRLENTVRWSWKPGDLAIWDNRATQHYAVADYDDQYRRLNRVTLAGDIPVDVYGERSRVIAG 284
                                    12        22        32        42        52        62     || 94       104       114       124       134       144       175       185       195       205       215       225       235       245       255       265       275         
                                                                                            68|                                                          152|                                                                                                              
                                                                                             91                                                           174                                                                                                              


Chain E from PDB  Type:PROTEIN  Length:250
                                                                                                                                                                                                                                                                                          
               SCOP domains d4j5ie_ E: automated matches                                                                                                                                                                                                                               SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee......eeee........hhhhhhhhhhhhhhhheeee......hhhhhhhhhhhhh....................eeeeeeee.......eeeeehhhhhhh.hhhhhhhhhhheeeee.....eeeee.eee......eee.....eeee...hhhhhhhhhhhhhhhhhh...eeee......eeeee...eeeee.........eeeeeee.............eeee.......... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4j5i E   2 VQVTVTKLGAHIGARIDGVRVGGDLSPATVSAINAALLEHKVIFFSGQDHLDDAGQLEFAELLGTPTVANSWHTDVTFVDRIPKASLLRAVTLPSYGGTTAWASTEAAYQQLPAPLRTLADNLWAVHTNRDYYEVEHPVVRVHPETGERVLLLGHFVKSFVGLKDTESAALFRLFQDRITRLENTVRWSWKPGDLAIWDNRATQHYAVADYDDQYRRLNRVTLAGDIPVDVYGERSRVIAGDASSYSPVD 293
                                    11        21        31        41        51        61       |92       102       112       122       132       142       152|      183       193       203       213       223       233       243       253       263       273       283       293
                                                                                              69|                                                          152|                                                                                                                       
                                                                                               91                                                           174                                                                                                                       


Chain F from PDB  Type:PROTEIN  Length:250
                                                                                                                                                                                                                                                                                          
               SCOP domains d4j5if_ F: automated matches                                                                                                                                                                                                                               SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee......eeee........hhhhhhhhhhhhhhhheeee......hhhhhhhhhhhhh...................eeeeeeee.......eeeeehhhhhhh.hhhhhhhhhhheeeee.....eeeee.eee......eee.....eeee...hhhhhhhhhhhhhhhhhh...eeee......eeeee...eeeee.........eeeeeee.............eeee............ Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4j5i F   3 QVTVTKLGAHIGARIDGVRVGGDLSPATVSAINAALLEHKVIFFSGQDHLDDAGQLEFAELLGTPTANSWHTDVTFVDRIPKASLLRAVTLPSYGGTTAWASTEAAYQQLPAPLRTLADNLWAVHTNRDYYEVEHPVVRVHPETGERVLLLGHFVKSFVGLKDTESAALFRLFQDRITRLENTVRWSWKPGDLAIWDNRATQHYAVADYDDQYRRLNRVTLAGDIPVDVYGERSRVIAGDASSYSPVDSP 295
                                    12        22        32        42        52        62     || 94       104       114       124       134       144       175       185       195       205       215       225       235       245       255       265       275       285       295
                                                                                            68|                                                          152|                                                                                                                         
                                                                                             91                                                           174                                                                                                                         


Chain G from PDB  Type:PROTEIN  Length:264
                                                                                                                                                                                                                                                                                                        
               SCOP domains d4j5ig_ G: automated matches                                                                                                                                                                                                                                             SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeee......eeee........hhhhhhhhhhhhhhhheeee......hhhhhhhhhhhhh...............eeee.................eeeeeeee.......eeeeehhhhhhh.hhhhhhhhhhheeeee.....eeeee.eee......eee.....eeee...hhhhhhhhhhhhhhhhhh...eeee......eeeee...eeeee.........eeeeeee.............eeee......... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4j5i G   3 QVTVTKLGAHIGARIDGVRVGGDLSPATVSAINAALLEHKVIFFSGQDHLDDAGQLEFAELLGTPTVAHPTLAEGAEQLLPIDANSWHTDVTFVDRIPKASLLRAVTLPSYGGTTAWASTEAAYQQLPAPLRTLADNLWAVHTNRDYYEVEHPVVRVHPETGERVLLLGHFVKSFVGLKDTESAALFRLFQDRITRLENTVRWSWKPGDLAIWDNRATQHYAVADYDDQYRRLNRVTLAGDIPVDVYGERSRVIAGDASSYSPV 292
                                    12        22        32        42        52        62        72        82  ||    97       107       117       127       137       147    || 178       188       198       208       218       228       238       248       258       268       278       288    
                                                                                                             85|                                                          152|                                                                                                                      
                                                                                                              91                                                           174                                                                                                                      


Chain H from PDB  Type:PROTEIN  Length:249
                                                                                                                                                                                                                                                                                         
               SCOP domains d4j5ih_ H: automated matches                                                                                                                                                                                                                              SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee......eeee........hhhhhhhhhhhhhhhheeee......hhhhhhhhhhhhh...................eeeeeeee.......eeeeehhhhhhh.hhhhhhhhhhheeeee.....eeeee.eee......eee.....eeee...hhhhhhhhhhhhhhhhhh...eeee......eeeee...eeeee.........eeeeeee.............eeee.......... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4j5i H   2 VQVTVTKLGAHIGARIDGVRVGGDLSPATVSAINAALLEHKVIFFSGQDHLDDAGQLEFAELLGTPTANSWHTDVTFVDRIPKASLLRAVTLPSYGGTTAWASTEAAYQQLPAPLRTLADNLWAVHTNRDYYEVEHPVVRVHPETGERVLLLGHFVKSFVGLKDTESAALFRLFQDRITRLENTVRWSWKPGDLAIWDNRATQHYAVADYDDQYRRLNRVTLAGDIPVDVYGERSRVIAGDASSYSPVD 293
                                    11        21        31        41        51        61      ||93       103       113       123       133       143       174       184       194       204       214       224       234       244       254       264       274       284         
                                                                                             68|                                                          152|                                                                                                                       
                                                                                              91                                                           174
   Legend:   → Mismatch (orange background)
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  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, 8)

Asymmetric Unit
(-)
Class: All beta proteins (24004)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4J5I)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4J5I)

(-) Gene Ontology  (5, 5)

Asymmetric Unit(hide GO term definitions)

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  4j5i
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 Related Entries

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(-) Related Entries Specified in the PDB File

3r1j ALPHA-KETOGLUTARATE-DEPENDENT TAURINE DIOXYGENASE FROM MYCOBACTERIUM AVIUM
3swt TAURINE CATABOLISM DIOXYGENASE, TAUD FROM MYCOBACTERIUM MARINUM RELATED ID: MYSMA.01188.A RELATED DB: TARGETTRACK