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(-) Description

Title :  MYCOBACTERIUM TUBERCULOSIS CYSM IN COMPLEX WITH THE UREA-SCAFFOLD INHIBITOR 5 [3-(3-(P-TOLYL)UREIDO) BENZOIC ACID]
 
Authors :  R. Schnell, S. Maric, G. Schneider
Date :  16 Feb 16  (Deposition) - 17 Aug 16  (Release) - 17 Aug 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.64
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
Keywords :  Cysteine Synthase, Mycobacterium Tuberculosis, 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, RV1336, MTCY130.21
    Mutation: YES
    Organism Scientific: MYCOBACTERIUM TUBERCULOSIS
    Organism Taxid: 1773
    Other Details: CYSM, OPS DEPENDENT CYSTEINE SYNTHASE, COVALENTLY BOUND PLP COFACTOR AT LYS51
    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, 10)

Asymmetric Unit (3, 10)
No.NameCountTypeFull Name
1AU64Ligand/Ion3-{[(4-METHYLPHENYL)CARBAMOYL]AMINO}BENZOIC ACID
2GOL2Ligand/IonGLYCEROL
3PLP4Ligand/IonPYRIDOXAL-5'-PHOSPHATE
Biological Unit 1 (3, 6)
No.NameCountTypeFull Name
1AU62Ligand/Ion3-{[(4-METHYLPHENYL)CARBAMOYL]AMINO}BENZOIC ACID
2GOL2Ligand/IonGLYCEROL
3PLP2Ligand/IonPYRIDOXAL-5'-PHOSPHATE
Biological Unit 2 (2, 4)
No.NameCountTypeFull Name
1AU62Ligand/Ion3-{[(4-METHYLPHENYL)CARBAMOYL]AMINO}BENZOIC ACID
2GOL-1Ligand/IonGLYCEROL
3PLP2Ligand/IonPYRIDOXAL-5'-PHOSPHATE

(-) Sites  (10, 10)

Asymmetric Unit (10, 10)
No.NameEvidenceResiduesDescription
01AC1SOFTWARELYS 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 , AU6 A:402 , GOL A:403 , HOH A:526 , HOH A:567 , HOH A:605binding site for residue PLP A 401
02AC2SOFTWARELYS 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:401 , GOL A:403 , HOH A:623binding site for residue AU6 A 402
03AC3SOFTWAREASN A:81 , ARG A:109 , TYR A:300 , PLP A:401 , AU6 A:402 , HOH A:564 , HOH A:597binding site for residue GOL A 403
04AC4SOFTWARELYS 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:401 , GOL B:403 , HOH B:594 , HOH B:637binding site for residue AU6 B 402
05AC5SOFTWARESER B:79 , AU6 B:402 , HOH B:577 , HOH B:637binding site for residue GOL B 403
06AC6SOFTWARELYS C:51 , THR C:78 , SER C:79 , 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:401 , HOH C:551 , HOH C:597binding site for residue AU6 C 402
07AC7SOFTWARELYS 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:401 , HOH D:565binding site for residue AU6 D 402
08AC8SOFTWARESER 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 , AU6 B:402 , HOH B:529 , HOH B:569 , HOH B:620binding site for Di-peptide PLP B 401 and LYS B 51
09AC9SOFTWARESER 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 , AU6 C:402 , HOH C:524 , HOH C:560 , HOH C:585binding site for Di-peptide PLP C 401 and LYS C 51
10AD1SOFTWARESER 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 , AU6 D:402 , HOH D:565 , HOH D:582 , HOH D:617 , HOH D:650binding site for Di-peptide PLP D 401 and LYS D 51

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5I6D)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 5I6D)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5I6D)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5I6D)

(-) Exons   (0, 0)

(no "Exon" information available for 5I6D)

(-) 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:285
                                                                                                                                                                                                                                                                                                                             
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhh.....eee................eeeeeee.........hhhhhhhhhhhhhhh.......eeeee..hhhhhhhhhhhhhhh.eeeeee....hhhhhhhhhhhh.eeee..hhhhhhhhhhhh..........hhhhhhhhhhhhhhhhhhhh....eeeee...hhhhhhhhhhhhhhh...eeeeeee.............eeeeehhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhh..eeeeeee..hhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5i6d A   3 RYDSLLQALGNTPLVGLQRLSPRWDDGRDGPHVRLWAKLEDRNPTGSIKDRPAVRMIEQAEADGLLRPGATILEPTSGNTGISLAMAARLKGYRLICVMPENTSVERRQLLELYGAQIIFSTAVATAKELAATNPSWVMLYQYGNPANTDSHYCGTGPELLADLPEITHFVAGLGTTGTLMGTGRFLREHVANVKIVAAEPRFVPELYDPEILTARYSVGAVDAVRRTRELVHTEGIFAGISTGAVLHAALGVGAGALAAGERADIALVVADAGWKYLSTGAYAG 308
                                    12        22        32        42        52        62        72        82        92       102       112       122||     139       149       159       169       179       189       199       209 ||    233       243       253       263       273       283       293       303     
                                                                                                                                                  123|                                                                             211|                                                                                  
                                                                                                                                                   131                                                                              226                                                                                  


Chain B from PDB  Type:PROTEIN  Length:287
                                                                                                                                                                                                                                                                                                                               
               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...ee.....hhhhhhhhhhhhhhhhhhhh....eeeee...hhhhhhhhhhhhhhh...eeeeeee.......hhhhh.eeeeehhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhh...eeeeeee..hhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5i6d B   3 RYDSLLQALGNTPLVGLQRLSPRWDGPHVRLWAKLEDRNPTGSIKDRPAVRMIEQAEADGLLRPGATILEPTSGNTGISLAMAARLKGYRLICVMPENTSVERRQLLELYGAQIIFSAAEGGSNTAVATAKELAATNPSWVMLYQYGNPANTDSHYCGTGPELLADLPEITHFVAGLGTTGTLMGTGRFLREHVANVKIVAAEPRFVPELYDPEILTARYSVGAVDAVRRTRELVHTEGIFAGISTGAVLHAALGVGAGALAAGERADIALVVADAGWKYLSTGAYA 307
                                    12        22    ||  36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206    || 230       240       250       260       270       280       290       300       
                                                   27|                                                                                                                                                                                211|                                                                                 
                                                    32                                                                                                                                                                                 226                                                                                 


Chain C from PDB  Type:PROTEIN  Length:290
                                                                                                                                                                                                                                                                                                                                  
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......hhhhh.....eee..............eeeeeee.........hhhhhhhhhhhhhhh.......eeeee..hhhhhhhhhhhhhhh.eeeeeee...hhhhhhhhhhh..eeeeehhhhhhhhhhhhhhhhhhhh...ee.....hhhhhhhhhhhhhhhhhhhh....eeeee...hhhhhhhhhhhhhhh...eeeeeee............eeeeehhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhh...eeeeeee..hhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5i6d C   0 HMARYDSLLQALGNTPLVGLQRLSPRWDDDGPHVRLWAKLEDRNPTGSIKDRPAVRMIEQAEADGLLRPGATILEPTSGNTGISLAMAARLKGYRLICVMPENTSVERRQLLELYGAQIIFSAAEGGSNTAVATAKELAATNPSWVMLYQYGNPANTDSHYCGTGPELLADLPEITHFVAGLGTTGTLMGTGRFLREHVANVKIVAAEPRVPELYDPEILTARYSVGAVDAVRRTRELVHTEGIFAGISTGAVLHAALGVGAGALAAGERADIALVVADAGWKYLSTGAY 306
                                     9        19        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211|      236       246       256       266       276       286       296       306
                                                       28|                                                                                                                                                                                 211|                                                                               
                                                        31                                                                                                                                                                                  227                                                                               


Chain D from PDB  Type:PROTEIN  Length:318
                                                                                                                                                                                                                                                                                                                                                              
               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...hhhh.ee...........hhhhh.eeeeehhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhh..eeeeeee...hhhhhhhh........hhhhhh..ee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5i6d D   3 RYDSLLQALGNTPLVGLQRLSPRWDDGRDGPHVRLWAKLEDRNPTGSIKDRPAVRMIEQAEADGLLRPGATILEPTSGNTGISLAMAARLKGYRLICVMPENTSVERRQLLELYGAQIIFSAASNTAVATAKELAATNPSWVMLYQYGNPANTDSHYCGTGPELLADLPEITHFVAGLGTTGTLMGTGRFLREHVANVKIVAAEPRYGEGVYALRNMDEGFVPELYDPEILTARYSVGAVDAVRRTRELVHTEGIFAGISTGAVLHAALGVGAGALAAGERADIALVVADAGWKYLSTGAYAGSLDDAETALEGQLWA 323
                                    12        22        32        42        52        62        72        82        92       102       112       122  ||   135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315        
                                                                                                                                                    125|                                                                                                                                                                                                  
                                                                                                                                                     129
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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 5I6D)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5I6D)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5I6D)

(-) 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 5i7a 5i7h 5i7o 5i7r 5iw8 5iwc

(-) Related Entries Specified in the PDB File

3dki LIGAND FREE STRUCTURE OF THE SAME PROTEIN
3fgp LIGAND FREE STRUCTURE OF THE SAME PROTEIN