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(-) Description

Title :  MYCOBACTERIUM TUBERCULOSIS CYSM IN COMPLEX WITH THE UREA-SCAFFOLD INHIBITOR 1 [3-(3-(3,4-DICHLOROPHENYL)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 :  2.08
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, Transferase, 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, MT1377
    Mutation: YES
    Organism Scientific: MYCOBACTERIUM TUBERCULOSIS
    Organism Taxid: 1773
    Other Details: LYS51 COVALENT MODIFICATION WITH PLP
    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  (2, 8)

Asymmetric Unit (2, 8)
No.NameCountTypeFull Name
168Q4Ligand/Ion3-{[(3,4-DICHLOROPHENYL)CARBAMOYL]AMINO}BENZOIC ACID
2PLP4Ligand/IonPYRIDOXAL-5'-PHOSPHATE
Biological Unit 1 (2, 4)
No.NameCountTypeFull Name
168Q2Ligand/Ion3-{[(3,4-DICHLOROPHENYL)CARBAMOYL]AMINO}BENZOIC ACID
2PLP2Ligand/IonPYRIDOXAL-5'-PHOSPHATE
Biological Unit 2 (2, 4)
No.NameCountTypeFull Name
168Q2Ligand/Ion3-{[(3,4-DICHLOROPHENYL)CARBAMOYL]AMINO}BENZOIC ACID
2PLP2Ligand/IonPYRIDOXAL-5'-PHOSPHATE

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELYS A:51 , THR A:78 , SER A:79 , ASN A:81 , THR A:82 , GLN A:151 , TYR A:152 , GLY A:184 , ALA A:208 , GLU A:209 , PRO A:210 , SER A:265 , ALA A:268 , PLP A:402 , HOH A:586binding site for residue 68Q A 401
2AC2SOFTWARELYS A:51 , ASN A:81 , GLY A:182 , GLY A:184 , THR A:185 , THR A:186 , GLY A:187 , THR A:188 , SER A:265 , ALA A:294 , ASP A:295 , 68Q A:401 , HOH A:534 , HOH A:578 , HOH A:601 , HOH A:622binding site for residue PLP A 402
3AC3SOFTWARELYS B:51 , THR B:78 , SER B:79 , 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:563 , HOH B:591binding site for residue 68Q B 401
4AC4SOFTWARELYS C:51 , THR C:78 , SER C:79 , GLY C:80 , ASN C:81 , THR C:82 , GLN C:151 , GLY C:184 , THR C:185 , GLU C:209 , PRO C:210 , SER C:265 , ALA C:268 , PLP C:402 , HOH C:561binding site for residue 68Q 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 , LEU D:219 , ASN D:221 , MET D:222 , SER D:265 , ALA D:268 , ALA D:323 , PLP D:402 , HOH D:532binding site for residue 68Q D 401
6AC6SOFTWARESER 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 , 68Q B:401 , HOH B:526 , HOH B:590 , HOH B:591 , HOH B:595binding site for Di-peptide PLP B 402 and LYS B 51
7AC7SOFTWARESER 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 , 68Q C:401 , HOH C:531 , HOH C:546 , HOH C:561binding site for Di-peptide PLP C 402 and LYS C 51
8AC8SOFTWARESER 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 , GLY D:184 , THR D:185 , THR D:186 , GLY D:187 , THR D:188 , SER D:265 , ALA D:294 , ASP D:295 , ALA D:323 , 68Q D:401 , HOH D:509 , HOH D:532 , HOH D:575 , HOH D:608binding site for Di-peptide PLP D 402 and LYS D 51

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5I7A)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 5I7A)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5I7A)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5I7A)

(-) Exons   (0, 0)

(no "Exon" information available for 5I7A)

(-) 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:281
                                                                                                                                                                                                                                                                                                                         
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhh.....eee................eeeeeee.........hhhhhhhhhhhhhhh.......eeeee..hhhhhhhhhhhhhhh.eeeeee....hhhhhhhhhhh..eeee..hhhhhhhhhhh..........hhhhhhhhhhhhhhhhhhhh....eeeee...hhhhhhhhhhhhhhh...eeeeeee............eeeeehhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhh..eeeeeee...hhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5i7a A   3 RYDSLLQALGNTPLVGLQRLSPRWDDGRDGPHVRLWAKLEDRNPTGSIKDRPAVRMIEQAEADGLLRPGATILEPTSGNTGISLAMAARLKGYRLICVMPENTSVERRQLLELYGAQIIFSAVATAKELAATNPSWVMLYQYGNPANTDSHYCGTGPELLADLPEITHFVAGLGTTGTLMGTGRFLREHVANVKIVAAEPRVPELYDPEILTARYSVGAVDAVRRTRELVHTEGIFAGISTGAVLHAALGVGAGALAAGERADIALVVADAGWKYLSTGAY 306
                                    12        22        32        42        52        62        72        82        92       102       112       122||     140       150       160       170       180       190       200       210||     235       245       255       265       275       285       295       305 
                                                                                                                                                  123|                                                                            211|                                                                               
                                                                                                                                                   132                                                                             227                                                                               


Chain B from PDB  Type:PROTEIN  Length:292
                                                                                                                                                                                                                                                                                                                                    
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhh.....eee................eeeeeee.........hhhhhhhhhhhhhhh.......eeeee..hhhhhhhhhhhhhhh.eeeeeee...hhhhhhhhhhh..eeeee...hhhhhhhhhhhhhhhhh..........hhhhhhhhhhhhhhhhhhhh....eeeee...hhhhhhhhhhhhhhh...eeeeeee........hhhhh.eeeeehhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhh...eeeeeee..hhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5i7a B   3 RYDSLLQALGNTPLVGLQRLSPRWDDGRDGPHVRLWAKLEDRNPTGSIKDRPAVRMIEQAEADGLLRPGATILEPTSGNTGISLAMAARLKGYRLICVMPENTSVERRQLLELYGAQIIFSAAEGGSNTAVATAKELAATNPSWVMLYQYGNPANTDSHYCGTGPELLADLPEITHFVAGLGTTGTLMGTGRFLREHVANVKIVAAEPRGFVPELYDPEILTARYSVGAVDAVRRTRELVHTEGIFAGISTGAVLHAALGVGAGALAAGERADIALVVADAGWKYLSTGAYA 307
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       225       235       245       255       265       275       285       295       305  
                                                                                                                                                                                                                                          211|                                                                                  
                                                                                                                                                                                                                                           225                                                                                  


Chain C from PDB  Type:PROTEIN  Length:283
                                                                                                                                                                                                                                                                                                                           
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhh.....eee...........eeeeeee.........hhhhhhhhhhhhhhh.......eeeee..hhhhhhhhhhhhhhh.eeeeeee...hhhhhhhhhhh..eeeee...hhhhhhhhhhhhhhhhh..........hhhhhhhhhhhhhhhhhhhh....eeeee...hhhhhhhhhhhhh.....eeeeeee...........eeeeehhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhh....eeeeeee..hhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5i7a C   3 RYDSLLQALGNTPLVGLQRLSPRWDDHVRLWAKLEDRNPTGSIKDRPAVRMIEQAEADGLLRPGATILEPTSGNTGISLAMAARLKGYRLICVMPENTSVERRQLLELYGAQIIFSAAEGGSNTAVATAKELAATNPSWVMLYQYGNPANTDSHYCGTGPELLADLPEITHFVAGLGTTGTLMGTGRFLREHVANVKIVAAEPRPELYDPEILTARYSVGAVDAVRRTRELVHTEGIFAGISTGAVLHAALGVGAGALAAGERADIALVVADAGWKYLSTGAY 306
                                    12        22     || 37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207   ||  233       243       253       263       273       283       293       303   
                                                    28|                                                                                                                                                                              211|                                                                              
                                                     34                                                                                                                                                                               228                                                                              


Chain D from PDB  Type:PROTEIN  Length:307
                                                                                                                                                                                                                                                                                                                                                   
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhh.....eee................eeeeeee.........hhhhhhhhhhhhhhh.......eeeee..hhhhhhhhhhhhhhh.eeeeeee...hhhhhhhhhhh..eeeee.....hhhhhhhhhhhhh..........hhhhhhhhhhhhhhhhhhhh....eeeee...hhhhhhhhhhhhhhh...eeeeeee..ee...........hhhhh.eeeeehhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhh...eeeeeee..hhhhhhhhh..........ee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5i7a D   3 RYDSLLQALGNTPLVGLQRLSPRWDDGRDGPHVRLWAKLEDRNPTGSIKDRPAVRMIEQAEADGLLRPGATILEPTSGNTGISLAMAARLKGYRLICVMPENTSVERRQLLELYGAQIIFSAAGSNTAVATAKELAATNPSWVMLYQYGNPANTDSHYCGTGPELLADLPEITHFVAGLGTTGTLMGTGRFLREHVANVKIVAAEPRALRNMDEGFVPELYDPEILTARYSVGAVDAVRRTRELVHTEGIFAGISTGAVLHAALGVGAGALAAGERADIALVVADAGWKYLSTGAYAGSLLEGQLWA 323
                                    12        22        32        42        52        62        72        82        92       102       112       122  ||   134       144       154       164       174       184       194       204      |220       230       240       250       260       270       280       290       300       310|      
                                                                                                                                                    125|                                                                                211|                                                                                         310|      
                                                                                                                                                     128                                                                                 218                                                                                          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 5I7A)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5I7A)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5I7A)

(-) Gene Ontology  (11, 16)

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 Related Entries

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

UniProtKB/Swiss-Prot
        CYSM_MYCTO | P9WP52: 3dki 3dwg 3dwi 3fgp
        CYSM_MYCTU | P9WP53: 3dki 3dwg 3dwi 3fgp 5i6d 5i7h 5i7o 5i7r 5iw8 5iwc

(-) Related Entries Specified in the PDB File

3dki PROTEIN STRUCTURE WITHOUT LIGAND BOUND.
3fgp PROTEIN STRUCTURE WITHOUT LIGAND BOUND.