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(-) Description

Title :  CRYSTAL STRUCTURE OF S114A MUTANT OF HSAD FROM MYCOBACTERIUM TUBERCULOSIS IN COMPLEX WITH 4,9DSHA
 
Authors :  N. A. Lack, K. C. Yam, E. D. Lowe, G. P. Horsman, R. Owen, E. Sim, L. D. Eltis
Date :  02 Oct 09  (Deposition) - 20 Oct 09  (Release) - 02 Feb 10  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (2x)
Biol. Unit 2:  B  (2x)
Keywords :  Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  N. A. Lack, K. C. Yam, E. D. Lowe, G. P. Horsman, R. Owen, E. Sim, L. D. Eltis
Characterization Of A C-C Hydrolase From Mycobacterium Tuberculosis Involved In Cholesterol Metabolism
J. Biol. Chem. V. 285 434 2010
PubMed-ID: 19875455  |  Reference-DOI: 10.1074/JBC.M109.058081

(-) Compounds

Molecule 1 - 2-HYDROXY-6-OXO-6-PHENYLHEXA-2,4-DIENOATE HYDROLASE BPHD
    ChainsA, B
    EC Number3.7.1.8
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPT7-7
    Expression System StrainDH5[ALPHA]
    Expression System Taxid668369
    Expression System Vector TypePLASMID
    MutationYES
    Organism ScientificMYCOBACTERIUM TUBERCULOSIS
    Organism Taxid83332
    StrainH37RV
    SynonymHSAD, 2-HYDROXY-6-PHENYLHEXA-2,4-DIENOIC ACID HYDROLASE

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit AB
Biological Unit 1 (2x)A 
Biological Unit 2 (2x) B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 4)

Asymmetric Unit (3, 4)
No.NameCountTypeFull Name
1GOL2Ligand/IonGLYCEROL
2KEM1Ligand/Ion(3E,5R)-8-[(1S,3AR,4R,7AS)-1-HYDROXY-7A-METHYL-5-OXOOCTAHYDRO-1H-INDEN-4-YL]-5-METHYL-2,6-DIOXOOCT-3-ENOATE
3SCN1Ligand/IonTHIOCYANATE ION
Biological Unit 1 (2, 4)
No.NameCountTypeFull Name
1GOL2Ligand/IonGLYCEROL
2KEM-1Ligand/Ion(3E,5R)-8-[(1S,3AR,4R,7AS)-1-HYDROXY-7A-METHYL-5-OXOOCTAHYDRO-1H-INDEN-4-YL]-5-METHYL-2,6-DIOXOOCT-3-ENOATE
3SCN2Ligand/IonTHIOCYANATE ION
Biological Unit 2 (2, 4)
No.NameCountTypeFull Name
1GOL2Ligand/IonGLYCEROL
2KEM2Ligand/Ion(3E,5R)-8-[(1S,3AR,4R,7AS)-1-HYDROXY-7A-METHYL-5-OXOOCTAHYDRO-1H-INDEN-4-YL]-5-METHYL-2,6-DIOXOOCT-3-ENOATE
3SCN-1Ligand/IonTHIOCYANATE ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY B:44 , GLY B:45 , GLY B:46 , ALA B:49 , ASN B:54 , ALA B:114 , LEU B:115 , LEU B:158 , ARG B:192 , PHE B:212 , HIS B:269 , TRP B:270 , HOH B:2093BINDING SITE FOR RESIDUE KEM B1289
2AC2SOFTWAREPHE A:9 , TRP A:52 , HOH A:2089 , HOH A:2090 , ARG B:167BINDING SITE FOR RESIDUE GOL A1289
3AC3SOFTWAREPHE B:15BINDING SITE FOR RESIDUE GOL B1290
4AC4SOFTWAREARG A:130 , TYR B:127 , PRO B:128 , ALA B:129 , ARG B:130BINDING SITE FOR RESIDUE SCN A1290

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Asp A:150 -Pro A:151
2Asp B:150 -Pro B:151

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 2WUF)

(-) 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:282
 aligned with HSAD_MYCTO | P9WNH4 from UniProtKB/Swiss-Prot  Length:291

    Alignment length:282
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286  
           HSAD_MYCTO     7 LTFESTSRFAEVDVDGPLKLHYHEAGVGNDQTVVLLHGGGPGAASWTNFSRNIAVLARHFHVLAVDQPGYGHSDKRAEHGQFNRYAAMALKGLFDQLGLGRVPLVGNSLGGGTAVRFALDYPARAGRLVLMGPGGLSINLFAPDPTEGVKRLSKFSVAPTRENLEAFLRVMVYDKNLITPELVDQRFALASTPESLTATRAMGKSFAGADFEAGMMWREVYRLRQPVLLIWGREDRVNPLDGALVALKTIPRAQLHVFGQCGHWVQVEKFDEFNKLTIEFLG 288
               SCOP domains d2wufa_ A: automated matches                                                                                                                                                                                                                                                               SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .hhhhheeeeee.....eeeeeeee......eeeee.......hhhhhh..hhhhhh...eeeee...............hhhhhhhhhhh............ee.......hhhhhhhhh......eee..................hhhhhhhhhh.hhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhh............hhhhhhhhh...eeeee...........hhhhhhhh..eeeee......hhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2wuf A   7 LTFESTSRFAEVDVDGPLKLHYHEAGVGNDQTVVLLHGGGPGAASWTNFSRNIAVLARHFHVLAVDQPGYGHSDKRAEHGQFNRYAAMALKGLFDQLGLGRVPLVGNALGGGTAVRFALDYPARAGRLVLMGPGGLSINLFAPDPTEGVKRLSKFSVAPTRENLEAFLRVMVYDKNLITPELVDQRFALASTPESLTATRAMGKSFAGADFEAGMMWREVYRLRQPVLLIWGREDRVNPLDGALVALKTIPRAQLHVFGQCGHWVQVEKFDEFNKLTIEFLG 288
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286  

Chain A from PDB  Type:PROTEIN  Length:282
 aligned with HSAD_MYCTU | P9WNH5 from UniProtKB/Swiss-Prot  Length:291

    Alignment length:282
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286  
           HSAD_MYCTU     7 LTFESTSRFAEVDVDGPLKLHYHEAGVGNDQTVVLLHGGGPGAASWTNFSRNIAVLARHFHVLAVDQPGYGHSDKRAEHGQFNRYAAMALKGLFDQLGLGRVPLVGNSLGGGTAVRFALDYPARAGRLVLMGPGGLSINLFAPDPTEGVKRLSKFSVAPTRENLEAFLRVMVYDKNLITPELVDQRFALASTPESLTATRAMGKSFAGADFEAGMMWREVYRLRQPVLLIWGREDRVNPLDGALVALKTIPRAQLHVFGQCGHWVQVEKFDEFNKLTIEFLG 288
               SCOP domains d2wufa_ A: automated matches                                                                                                                                                                                                                                                               SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .hhhhheeeeee.....eeeeeeee......eeeee.......hhhhhh..hhhhhh...eeeee...............hhhhhhhhhhh............ee.......hhhhhhhhh......eee..................hhhhhhhhhh.hhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhh............hhhhhhhhh...eeeee...........hhhhhhhh..eeeee......hhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2wuf A   7 LTFESTSRFAEVDVDGPLKLHYHEAGVGNDQTVVLLHGGGPGAASWTNFSRNIAVLARHFHVLAVDQPGYGHSDKRAEHGQFNRYAAMALKGLFDQLGLGRVPLVGNALGGGTAVRFALDYPARAGRLVLMGPGGLSINLFAPDPTEGVKRLSKFSVAPTRENLEAFLRVMVYDKNLITPELVDQRFALASTPESLTATRAMGKSFAGADFEAGMMWREVYRLRQPVLLIWGREDRVNPLDGALVALKTIPRAQLHVFGQCGHWVQVEKFDEFNKLTIEFLG 288
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286  

Chain B from PDB  Type:PROTEIN  Length:282
 aligned with HSAD_MYCTO | P9WNH4 from UniProtKB/Swiss-Prot  Length:291

    Alignment length:282
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286  
           HSAD_MYCTO     7 LTFESTSRFAEVDVDGPLKLHYHEAGVGNDQTVVLLHGGGPGAASWTNFSRNIAVLARHFHVLAVDQPGYGHSDKRAEHGQFNRYAAMALKGLFDQLGLGRVPLVGNSLGGGTAVRFALDYPARAGRLVLMGPGGLSINLFAPDPTEGVKRLSKFSVAPTRENLEAFLRVMVYDKNLITPELVDQRFALASTPESLTATRAMGKSFAGADFEAGMMWREVYRLRQPVLLIWGREDRVNPLDGALVALKTIPRAQLHVFGQCGHWVQVEKFDEFNKLTIEFLG 288
               SCOP domains d2wufb_ B: automated matches                                                                                                                                                                                                                                                               SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .hhhhheeeeee.....eeeeeeee......eeeee.......hhhhhhhhhhhhhh...eeeee...............hhhhhhhhhhh............ee.......hhhhhhhhh......eee..................hhhhhhhhhh.hhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhh............hhhhhhhhh...eeeee...........hhhhhhhh..eeeee......hhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2wuf B   7 LTFESTSRFAEVDVDGPLKLHYHEAGVGNDQTVVLLHGGGPGAASWTNFSRNIAVLARHFHVLAVDQPGYGHSDKRAEHGQFNRYAAMALKGLFDQLGLGRVPLVGNALGGGTAVRFALDYPARAGRLVLMGPGGLSINLFAPDPTEGVKRLSKFSVAPTRENLEAFLRVMVYDKNLITPELVDQRFALASTPESLTATRAMGKSFAGADFEAGMMWREVYRLRQPVLLIWGREDRVNPLDGALVALKTIPRAQLHVFGQCGHWVQVEKFDEFNKLTIEFLG 288
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286  

Chain B from PDB  Type:PROTEIN  Length:282
 aligned with HSAD_MYCTU | P9WNH5 from UniProtKB/Swiss-Prot  Length:291

    Alignment length:282
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286  
           HSAD_MYCTU     7 LTFESTSRFAEVDVDGPLKLHYHEAGVGNDQTVVLLHGGGPGAASWTNFSRNIAVLARHFHVLAVDQPGYGHSDKRAEHGQFNRYAAMALKGLFDQLGLGRVPLVGNSLGGGTAVRFALDYPARAGRLVLMGPGGLSINLFAPDPTEGVKRLSKFSVAPTRENLEAFLRVMVYDKNLITPELVDQRFALASTPESLTATRAMGKSFAGADFEAGMMWREVYRLRQPVLLIWGREDRVNPLDGALVALKTIPRAQLHVFGQCGHWVQVEKFDEFNKLTIEFLG 288
               SCOP domains d2wufb_ B: automated matches                                                                                                                                                                                                                                                               SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .hhhhheeeeee.....eeeeeeee......eeeee.......hhhhhhhhhhhhhh...eeeee...............hhhhhhhhhhh............ee.......hhhhhhhhh......eee..................hhhhhhhhhh.hhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhh............hhhhhhhhh...eeeee...........hhhhhhhh..eeeee......hhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2wuf B   7 LTFESTSRFAEVDVDGPLKLHYHEAGVGNDQTVVLLHGGGPGAASWTNFSRNIAVLARHFHVLAVDQPGYGHSDKRAEHGQFNRYAAMALKGLFDQLGLGRVPLVGNALGGGTAVRFALDYPARAGRLVLMGPGGLSINLFAPDPTEGVKRLSKFSVAPTRENLEAFLRVMVYDKNLITPELVDQRFALASTPESLTATRAMGKSFAGADFEAGMMWREVYRLRQPVLLIWGREDRVNPLDGALVALKTIPRAQLHVFGQCGHWVQVEKFDEFNKLTIEFLG 288
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286  

   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, 2)

Asymmetric Unit

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2WUF)

(-) Gene Ontology  (11, 17)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (HSAD_MYCTU | P9WNH5)
molecular function
    GO:0018774    2,6-dioxo-6-phenylhexa-3-enoate hydrolase activity    Catalysis of the reaction: 2,6-dioxo-6-phenylhexa-3-enoate + H2O = benzoate + 2-oxopent-4-enoate.
    GO:0034820    4,9-DSHA hydrolase activity    Catalysis of the reaction: (3E,1Z)-4,5-9,10-diseco-3-hydroxy-5,9,17-trioxoandrosta-1(10),2-diene-4-oate + H2O = (2E,4E)-2-hydroxyhexa-2,4-dienoate + 9,17-dioxo-1,2,3,4,10,19-hexanorandrostan-5-oate + H+.
    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: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:0019439    aromatic compound catabolic process    The chemical reactions and pathways resulting in the breakdown of aromatic compounds, any substance containing an aromatic carbon ring.
    GO:0044117    growth of symbiont in host    The increase in size or mass of an organism, occurring within the cells or tissues of the host organism. This may (but not necessarily) include a filamentous growth form, and also can include secretion of proteases and lipases to break down host tissue. The host is defined as the larger of the organisms involved in a symbiotic interaction.
    GO:0016042    lipid catabolic process    The chemical reactions and pathways resulting in the breakdown of lipids, compounds soluble in an organic solvent but not, or sparingly, in an aqueous solvent.
    GO:0006629    lipid metabolic process    The chemical reactions and pathways involving lipids, compounds soluble in an organic solvent but not, or sparingly, in an aqueous solvent. Includes fatty acids; neutral fats, other fatty-acid esters, and soaps; long-chain (fatty) alcohols and waxes; sphingoids and other long-chain bases; glycolipids, phospholipids and sphingolipids; and carotenes, polyprenols, sterols, terpenes and other isoprenoids.
    GO:0006694    steroid biosynthetic process    The chemical reactions and pathways resulting in the formation of steroids, compounds with a 1,2,cyclopentanoperhydrophenanthrene nucleus; includes de novo formation and steroid interconversion by modification.
cellular component
    GO:0005618    cell wall    The rigid or semi-rigid envelope lying outside the cell membrane of plant, fungal, most prokaryotic cells and some protozoan parasites, maintaining their shape and protecting them from osmotic lysis. In plants it is made of cellulose and, often, lignin; in fungi it is composed largely of polysaccharides; in bacteria it is composed of peptidoglycan; in protozoan parasites such as Giardia species, it's made of carbohydrates and proteins.
    GO:0005886    plasma membrane    The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.

Chain A,B   (HSAD_MYCTO | P9WNH4)
molecular function
    GO:0018774    2,6-dioxo-6-phenylhexa-3-enoate hydrolase activity    Catalysis of the reaction: 2,6-dioxo-6-phenylhexa-3-enoate + H2O = benzoate + 2-oxopent-4-enoate.
    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.
biological process
    GO:0019439    aromatic compound catabolic process    The chemical reactions and pathways resulting in the breakdown of aromatic compounds, any substance containing an aromatic carbon ring.
    GO:0016042    lipid catabolic process    The chemical reactions and pathways resulting in the breakdown of lipids, compounds soluble in an organic solvent but not, or sparingly, in an aqueous solvent.
    GO:0006629    lipid metabolic process    The chemical reactions and pathways involving lipids, compounds soluble in an organic solvent but not, or sparingly, in an aqueous solvent. Includes fatty acids; neutral fats, other fatty-acid esters, and soaps; long-chain (fatty) alcohols and waxes; sphingoids and other long-chain bases; glycolipids, phospholipids and sphingolipids; and carotenes, polyprenols, sterols, terpenes and other isoprenoids.
    GO:0006694    steroid biosynthetic process    The chemical reactions and pathways resulting in the formation of steroids, compounds with a 1,2,cyclopentanoperhydrophenanthrene nucleus; includes de novo formation and steroid interconversion by modification.

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 Related Entries

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

UniProtKB/Swiss-Prot
        HSAD_MYCTO | P9WNH42vf2 2wud 2wue 2wug 5jz9
        HSAD_MYCTU | P9WNH52vf2 2wud 2wue 2wug 5jzb 5jzs

(-) Related Entries Specified in the PDB File

2vf2 X-RAY CRYSTAL STRUCTURE OF HSAD FROM MYCOBACTERIUM TUBERCULOSIS
2wud CRYSTAL STRUCTURE OF S114A MUTANT OF HSAD FROM MYCOBACTERIUM TUBERCULOSIS
2wue CRYSTAL STRUCTURE OF S114A MUTANT OF HSAD FROM MYCOBACTERIUM TUBERCULOSIS IN COMPLEX WITH HOPODA
2wug CRYSTAL STRUCTURE OF S114A MUTANT OF HSAD FROM MYCOBACTERIUM TUBERCULOSIS IN COMPLEX WITH HOPDA