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(-) Description

Title :  MYCOBACTERIUM TUBERCULOSIS CYSM IN COMPLEX WITH THE UREA-SCAFFOLD INHIBITOR 2 [3-(3-([1,1'-BIPHENYL]-3-YL)UREIDO)BENZOIC ACID]
 
Authors :  R. Schnell, S. Maric, G. Schneider
Date :  18 Feb 16  (Deposition) - 17 Aug 16  (Release) - 17 Aug 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.73
Chains :  Asym./Biol. Unit :  A,B
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: B, A
    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: 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

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (3, 9)
No.NameCountTypeFull Name
168W2Ligand/Ion3-{[([1,1'-BIPHENYL]-3-YL)CARBAMOYL]AMINO}BENZOIC ACID
2ACT5Ligand/IonACETATE ION
3PLP2Ligand/IonPYRIDOXAL-5'-PHOSPHATE

(-) Sites  (9, 9)

Asymmetric Unit (9, 9)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELYS B:51 , ASN B:81 , 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 , 68W B:402 , HOH B:510 , HOH B:548 , HOH B:564binding site for residue PLP B 401
2AC2SOFTWARELYS B:51 , GLY B:80 , ASN B:81 , THR B:82 , GLY B:184 , ALA B:208 , PRO B:210 , ALA B:218 , ARG B:220 , VAL B:242 , ALA B:247 , ILE B:264 , SER B:265 , ALA B:268 , PLP B:401 , HOH B:514 , HOH B:538 , HOH B:539 , HOH B:569binding site for residue 68W B 402
3AC3SOFTWARELEU A:7 , PRO A:46 , ASP B:43 , ARG B:44binding site for residue ACT B 403
4AC4SOFTWARETRP A:298 , ASN B:45 , PRO B:46 , GLY B:48 , HOH B:571binding site for residue ACT B 404
5AC5SOFTWARETHR B:78 , SER B:79 , TYR B:152 , ASN B:221 , HOH B:514binding site for residue ACT B 405
6AC6SOFTWARELYS A:51 , THR A:78 , SER A:79 , ASN A:81 , THR A:82 , GLN A:151 , TYR A:152 , GLY A:182 , GLY A:184 , ALA A:208 , PRO A:210 , VAL A:242 , ALA A:247 , ILE A:264 , SER A:265 , ALA A:268 , PLP A:401 , HOH A:564binding site for residue 68W A 402
7AC7SOFTWAREASP A:43 , ASN A:45 , PRO A:46 , GLY A:48 , HOH A:524 , TRP B:298binding site for residue ACT A 403
8AC8SOFTWARELEU A:41 , ASP A:43 , ARG A:44 , LEU B:7 , PRO B:46binding site for residue ACT A 404
9AC9SOFTWARESER A:49 , ILE A:50 , ASP A:52 , ARG A:53 , PRO A:54 , ALA A:55 , ASN A:81 , THR A:82 , SER A:85 , 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 , 68W A:402 , HOH A:519 , HOH A:540 , HOH A:542binding site for Di-peptide PLP A 401 and LYS A 51

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5I7R)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 5I7R)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5I7R)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5I7R)

(-) Exons   (0, 0)

(no "Exon" information available for 5I7R)

(-) Sequences/Alignments

Asymmetric/Biological 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:306
                                                                                                                                                                                                                                                                                                                                                  
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ....hhhhh.....eee................eeeeeee.........hhhhhhhhhhhhhhh.......eeeee..hhhhhhhhhhhhhhh.eeeeeee...hhhhhhhhhhhh.eeeeehhhhhhhhhhhhhhhhhhhh...ee.....hhhhhhhhhhhhhhhhhhhh....eeeee...hhhhhhhhhhhhhhh...eeeeee.......hhhhh.eeee.hhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhh...eeeeeee..hhhhhhhhh....hhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5i7r A   2 ARYDSLLQALGNTPLVGLQRLSPRWDDGRDGPHVRLWAKLEDRNPTGSIKDRPAVRMIEQAEADGLLRPGATILEPTSGNTGISLAMAARLKGYRLICVMPENTSVERRQLLELYGAQIIFSAAEGGSNTAVATAKELAATNPSWVMLYQYGNPANTDSHYCGTGPELLADLPEITHFVAGLGTTGTLMGTGRFLREHVANVKIVAAEPFVPELYDPEILTARYSVGAVDAVRRTRELVHTEGIFAGISTGAVLHAALGVGAGALAAGERADIALVVADAGWKYLSTGAYAGSLDDAETALEGQLW 322
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       226       236       246       256       266       276       286       296       306       316      
                                                                                                                                                                                                                                          210|                                                                                                
                                                                                                                                                                                                                                           226                                                                                                


Chain B from PDB  Type:PROTEIN  Length:316
                                                                                                                                                                                                                                                                                                                                                            
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .ee.hhhhh.....eee................eeeeeee.........hhhhhhhhhhhhhhh.......eeeee..hhhhhhhhhhhhhhh.eeeeeee...hhhhhhhhhhh..eeeeehhhhhhhhhhhhhhhhhhh...eee.....hhhhhhhhhhhhhhhhhhhh....eeeee...hhhhhhhhhhhhhhh...eeeeeee.....................hhhhh.eeeeehhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhh...eeeeeee...hhhhhhhh....hhhhhh... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5i7r B   2 ARYDSLLQALGNTPLVGLQRLSPRWDDGRDGPHVRLWAKLEDRNPTGSIKDRPAVRMIEQAEADGLLRPGATILEPTSGNTGISLAMAARLKGYRLICVMPENTSVERRQLLELYGAQIIFSAAEGGSNTAVATAKELAATNPSWVMLYQYGNPANTDSHYCGTGPELLADLPEITHFVAGLGTTGTLMGTGRFLREHVANVKIVAAEPRYGEGVYALRNMDEGFVPELYDPEILTARYSVGAVDAVRRTRELVHTEGIFAGISTGAVLHAALGVGAGALAAGERADIALVVADAGWKYLSTGAYAGSLDDAETAL 317
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311
   Legend:   → Mismatch (orange background)
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    → 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  (0, 0)

(no "SCOP Domain" information available for 5I7R)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5I7R)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5I7R)

(-) Gene Ontology  (11, 11)

Asymmetric/Biological Unit(hide GO term definitions)

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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 5i7h 5i7o 5iw8 5iwc

(-) Related Entries Specified in the PDB File

3dki CYSM WITHOUT LIGANDS BOUND
3fgp