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(-) Description

Title :  MYCOBACTERIUM TUBERCULOSIS CYSM IN COMPLEX WITH THE UREA-SCAFFOLD INHIBITOR 6 [3-(3-(4-BROMOPHENYL)UREIDO)BENZOIC ACID]
 
Authors :  R. Schnell, S. Maric, G. Schneider
Date :  17 Feb 16  (Deposition) - 17 Aug 16  (Release) - 17 Aug 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.57
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
Keywords :  Mycobacterium Tuberculosis, Cysteine Biosynthesis, Sulphur Metabolism, Inhibitor, Lyase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  K. Brunner, S. Maric, R. S. Reshma, H. Almqvist, B. Seashore-Ludlow, A. L. Gustavsson, O. Poyraz, P. Yogeeswari, T. Lundback, M. Vallin, D. Sriram, R. Schnell, G. Schneider
Inhibitors Of The Cysteine Synthase Cysm With Antibacterial Potency Against Dormant Mycobacterium Tuberculosis.
J. Med. Chem. V. 59 6848 2016
PubMed-ID: 27379713  |  Reference-DOI: 10.1021/ACS.JMEDCHEM.6B00674

(-) Compounds

Molecule 1 - O-PHOSPHOSERINE SULFHYDRYLASE
    Chains: A, B, C, D
    EC Number: 2.5.1.113
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PET28A
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: CYSM, RV1336, MTCY130.21
    Mutation: YES
    Organism Scientific: MYCOBACTERIUM TUBERCULOSIS
    Organism Taxid: 83332
    Other Details: LYS51 COVALENT MODIFICATION WITH PLP
    Strain: ATCC 25618 / H37RV
    Synonym: OPS SULFHYDRYLASE,CYSO-THIOCARBOXYLATE-DEPENDENT CYSTEINE SYNTHASE,CYSTEINE SYNTHASE B,CSASE B,O-PHOSPHOSERINE-SPECIFIC CYSTEINE SYNTHASE,[CYSO SULFUR-CARRIER PROTEIN]-THIOCARBOXYLATE- DEPENDENT CYSTEINE SYNTHASE

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): AB  
Biological Unit 2 (1x):   CD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 9)

Asymmetric Unit (3, 9)
No.NameCountTypeFull Name
168V4Ligand/Ion3-{[(4-BROMOPHENYL)CARBAMOYL]AMINO}BENZOIC ACID
2CL1Ligand/IonCHLORIDE ION
3PLP4Ligand/IonPYRIDOXAL-5'-PHOSPHATE
Biological Unit 1 (2, 4)
No.NameCountTypeFull Name
168V2Ligand/Ion3-{[(4-BROMOPHENYL)CARBAMOYL]AMINO}BENZOIC ACID
2CL-1Ligand/IonCHLORIDE ION
3PLP2Ligand/IonPYRIDOXAL-5'-PHOSPHATE
Biological Unit 2 (2, 4)
No.NameCountTypeFull Name
168V2Ligand/Ion3-{[(4-BROMOPHENYL)CARBAMOYL]AMINO}BENZOIC ACID
2CL-1Ligand/IonCHLORIDE ION
3PLP2Ligand/IonPYRIDOXAL-5'-PHOSPHATE

(-) Sites  (9, 9)

Asymmetric Unit (9, 9)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELYS A:51 , THR A:78 , SER A:79 , GLY A:80 , ASN A:81 , THR A:82 , GLN A:151 , TYR A:152 , GLY A:184 , THR A:185 , ALA A:208 , GLU A:209 , PRO A:210 , SER A:265 , ALA A:268 , PLP A:402 , HOH A:526binding site for residue 68V A 401
2AC2SOFTWARELYS A:51 , ASN A:81 , GLY A:182 , LEU A:183 , GLY A:184 , THR A:185 , THR A:186 , GLY A:187 , THR A:188 , SER A:265 , ALA A:294 , ASP A:295 , 68V A:401 , HOH A:516 , HOH A:524binding site for residue PLP A 402
3AC3SOFTWARELYS B:51 , THR B:78 , SER B:79 , GLY B:80 , ASN B:81 , THR B:82 , GLN B:151 , TYR B:152 , GLY B:184 , THR B:185 , ALA B:208 , GLU B:209 , PRO B:210 , SER B:265 , ALA B:268 , PLP B:402 , HOH B:520 , HOH B:537binding site for residue 68V B 401
4AC4SOFTWARELYS C:51 , THR C:78 , SER C:79 , GLY C:80 , ASN C:81 , THR C:82 , GLN C:151 , TYR C:152 , GLY C:184 , ALA C:208 , GLU C:209 , PRO C:210 , SER C:265 , ALA C:268 , PLP C:402binding site for residue 68V C 401
5AC5SOFTWARELYS D:51 , THR D:78 , SER D:79 , ASN D:81 , THR D:82 , GLN D:151 , TYR D:152 , GLY D:182 , GLY D:184 , ALA D:208 , GLU D:209 , PRO D:210 , ASN D:221 , SER D:265 , ALA D:268 , ALA D:323 , PLP D:403 , HOH D:502 , HOH D:508binding site for residue 68V D 401
6AC6SOFTWAREARG D:220 , ASN D:221 , MET D:222binding site for residue CL D 402
7AC7SOFTWARESER B:49 , ILE B:50 , ASP B:52 , ARG B:53 , PRO B:54 , ALA B:55 , ASN B:81 , THR B:82 , SER B:85 , GLY B:182 , GLY B:184 , THR B:185 , THR B:186 , GLY B:187 , THR B:188 , SER B:265 , ALA B:294 , ASP B:295 , 68V B:401 , HOH B:512 , HOH B:523 , HOH B:525binding site for Di-peptide PLP B 402 and LYS B 51
8AC8SOFTWARESER C:49 , ILE C:50 , ASP C:52 , ARG C:53 , PRO C:54 , ALA C:55 , ASN C:81 , THR C:82 , SER C:85 , GLY C:182 , GLY C:184 , THR C:185 , THR C:186 , GLY C:187 , THR C:188 , SER C:265 , ALA C:294 , ASP C:295 , 68V C:401 , HOH C:504 , HOH C:513 , HOH C:535binding site for Di-peptide PLP C 402 and LYS C 51
9AC9SOFTWARESER D:49 , ILE D:50 , ASP D:52 , ARG D:53 , PRO D:54 , ALA D:55 , ASN D:81 , THR D:82 , SER D:85 , GLY D:182 , LEU D:183 , GLY D:184 , THR D:185 , THR D:186 , GLY D:187 , THR D:188 , SER D:265 , ALA D:294 , ASP D:295 , 68V D:401 , HOH D:504 , HOH D:517 , HOH D:534binding site for Di-peptide PLP D 403 and LYS D 51

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5I7H)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 5I7H)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5I7H)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5I7H)

(-) Exons   (0, 0)

(no "Exon" information available for 5I7H)

(-) 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:280
                                                                                                                                                                                                                                                                                                                        
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhh.....eeee...............eeeeeee.........hhhhhhhhhhhhhhh.......eeeee..hhhhhhhhhhhhhhh.eeeee.....hhhhhhhhhhhh.eee..hhhhhhhhhhh..........hhhhhhhhhhhhhhhhhhhh....eeeee...hhhhhhhhhhhhhhh...eeeeeee............eeeeehhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhh...eeeeeee...hhhhh..... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5i7h A   3 RYDSLLQALGNTPLVGLQRLSPRWDDGRDGPHVRLWAKLEDRNPTGSIKDRPAVRMIEQAEADGLLRPGATILEPTSGNTGISLAMAARLKGYRLICVMPENTSVERRQLLELYGAQIIFAVATAKELAATNPSWVMLYQYGNPANTDSHYCGTGPELLADLPEITHFVAGLGTTGTLMGTGRFLREHVANVKIVAAEPRVPELYDPEILTARYSVGAVDAVRRTRELVHTEGIFAGISTGAVLHAALGVGAGALAAGERADIALVVADAGWKYLSTGAY 306
                                    12        22        32        42        52        62        72        82        92       102       112       122|      141       151       161       171       181       191       201       211|      236       246       256       266       276       286       296       306
                                                                                                                                                 122|                                                                            211|                                                                               
                                                                                                                                                  132                                                                             227                                                                               


Chain B from PDB  Type:PROTEIN  Length:291
                                                                                                                                                                                                                                                                                                                                   
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .ee.hhhhh.....eeee..............eeeeeee.........hhhhhhhhhhhhhhhh......eeeee..hhhhhhhhhhhhhhh.eeeeeee...hhhhhhhhhhhh.eeeee...hhhhhhhhhhhhhhhh....ee.....hhhhhhhhhhhhhhhhhhhh....eeeee...hhhhhhhhhhhhhhh...eeeeeee.......hhhhh.eeeeehhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhh...eeeeeee..hhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5i7h B   2 ARYDSLLQALGNTPLVGLQRLSPRWDDGDGPHVRLWAKLEDRNPTGSIKDRPAVRMIEQAEADGLLRPGATILEPTSGNTGISLAMAARLKGYRLICVMPENTSVERRQLLELYGAQIIFSAAEGGSNTAVATAKELAATNPSWVMLYQYGNPANTDSHYCGTGPELLADLPEITHFVAGLGTTGTLMGTGRFLREHVANVKIVAAEPRFVPELYDPEILTARYSVGAVDAVRRTRELVHTEGIFAGISTGAVLHAALGVGAGALAAGERADIALVVADAGWKYLSTGAYA 307
                                    11        21       |32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       226       236       246       256       266       276       286       296       306 
                                                      29|                                                                                                                                                                                 211|                                                                                 
                                                       31                                                                                                                                                                                  226                                                                                 


Chain C from PDB  Type:PROTEIN  Length:284
                                                                                                                                                                                                                                                                                                                            
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhh.....eeee..........eeeeeee.........hhhhhhhhhhhhhhh.......eeeee..hhhhhhhhhhhhhhh.eeeeeee...hhhhhhhhhhh..eeeee....hhhhhhhhhhhhhhhh..........hhhhhhhhhhhhhhhhhhhh....eeeee...hhhhhhhhhhhhh.....eeeeee.............eee.hhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhh...eeeeeee..hhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5i7h C   2 ARYDSLLQALGNTPLVGLQRLSPRWDDHVRLWAKLEDRNPTGSIKDRPAVRMIEQAEADGLLRPGATILEPTSGNTGISLAMAARLKGYRLICVMPENTSVERRQLLELYGAQIIFSAAEGGSNTAVATAKELAATNPSWVMLYQYGNPANTDSHYCGTGPELLADLPEITHFVAGLGTTGTLMGTGRFLREHVANVKIVAAEPRPELYDPEILTARYSVGAVDAVRRTRELVHTEGIFAGISTGAVLHAALGVGAGALAAGERADIALVVADAGWKYLSTGAY 306
                                    11        21      ||36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206    || 232       242       252       262       272       282       292       302    
                                                     28|                                                                                                                                                                              211|                                                                              
                                                      34                                                                                                                                                                               228                                                                              


Chain D from PDB  Type:PROTEIN  Length:304
                                                                                                                                                                                                                                                                                                                                                
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .............eee..............eeeeeee.........hhhhhhhhhhhhhh........eeeee..hhhhhhhhhhhhhhh.eeeeeee...hhhhhhhhhhhh.eeeee...hhhhhhhhhhhhh..........hhhhhhhhhhhhhhhhhhhh....eeeee...hhhhhhhhhhhhhhh...eeeeeee...ee...........hhhhh.eeeeehhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhh...eeeeeee..hhhhhhhhh..........ee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5i7h D   3 RYDSLLQALGNTPLVGLQRLSPRWDDDGPHVRLWAKLEDRNPTGSIKDRPAVRMIEQAEADGLLRPGATILEPTSGNTGISLAMAARLKGYRLICVMPENTSVERRQLLELYGAQIIFSAANTAVATAKELAATNPSWVMLYQYGNPANTDSHYCGTGPELLADLPEITHFVAGLGTTGTLMGTGRFLREHVANVKIVAAEPRYALRNMDEGFVPELYDPEILTARYSVGAVDAVRRTRELVHTEGIFAGISTGAVLHAALGVGAGALAAGERADIALVVADAGWKYLSTGAYAGSLLEGQLWA 323
                                    12        22     || 34        44        54        64        74        84        94       104       114       124||     138       148       158       168       178       188       198       208  ||   223       233       243       253       263       273       283       293       303      |319    
                                                    28|                                                                                           125|                                                                              211|                                                                                          310|      
                                                     31                                                                                            130                                                                               217                                                                                           317
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  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (0, 0)

(no "SCOP Domain" information available for 5I7H)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5I7H)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5I7H)

(-) Gene Ontology  (11, 11)

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 Related Entries

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

UniProtKB/Swiss-Prot
        CYSM_MYCTU | P9WP53: 3dki 3dwg 3dwi 3fgp 5i6d 5i7a 5i7o 5i7r 5iw8 5iwc

(-) Related Entries Specified in the PDB File

3dki CYSM WITHOUT LIGAND BOUND
3fgp CYSM WITHOUT LIGAND BOUND