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(-) Description

Title :  MYCOBACTERIUM TUBERCULOSIS CYSM IN COMPLEX WITH THE UREA-SCAFFOLD INHIBITOR 4 [5-(3-([1,1'-BIPHENYL]-3-YL)UREIDO)-2-HYDROXYBENZOIC ACID]
 
Authors :  K. Brunner, R. Schnell, G. Schneider
Date :  22 Mar 16  (Deposition) - 17 Aug 16  (Release) - 17 Aug 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.04
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: A, B
    EC Number: 2.5.1.113
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Gene: CYSM, RV1336, MTCY130.21
    Mutation: YES
    Organism Scientific: MYCOBACTERIUM TUBERCULOSIS (STRAIN ATCC 25618 / H37RV)
    Organism Taxid: 83332
    Other Details: T2A MUTATION. 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, 5)

Asymmetric/Biological Unit (3, 5)
No.NameCountTypeFull Name
16EC2Ligand/Ion5-{[([1,1'-BIPHENYL]-3-YL)CARBAMOYL]AMINO}-2-HYDROXYBENZOIC ACID
2NA1Ligand/IonSODIUM ION
3PLP2Ligand/IonPYRIDOXAL-5'-PHOSPHATE

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELYS A:51 , GLY A:80 , ASN A:81 , THR A:82 , GLN A:151 , TYR A:152 , 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:403 , HOH A:567 , HOH A:606 , HOH A:637binding site for residue 6EC A 401
2AC2SOFTWAREALA A:140 , ASN A:143 , TRP A:146 , HOH A:603 , HOH A:654binding site for residue NA A 402
3AC3SOFTWARELYS 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 , 6EC A:401 , HOH A:521 , HOH A:556 , HOH A:583binding site for residue PLP A 403
4AC4SOFTWARELYS B:51 , SER B:79 , GLY B:80 , ASN B:81 , THR B:82 , ARG B:109 , GLN B:151 , TYR B:152 , GLY B:184 , ALA B:208 , PRO B:210 , LEU B:219 , ASN B:221 , VAL B:242 , ALA B:247 , ALA B:268 , PLP B:402 , HOH B:580binding site for residue 6EC B 401
5AC5SOFTWARESER 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 , 6EC B:401 , HOH B:551 , HOH B:608 , HOH B:649binding site for Di-peptide PLP B 402 and LYS B 51

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5IW8)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 5IW8)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5IW8)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5IW8)

(-) Exons   (0, 0)

(no "Exon" information available for 5IW8)

(-) 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:299
                                                                                                                                                                                                                                                                                                                                           
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhh....eee................eeeeeee.hhh.....hhhhhhhhhhhhhhh.......eeee...hhhhhhhhhhhhhh..eeeeeee...hhhhhhhhhhh..eeeee...hhhhhhhhhhhhhhhh...eee.....hhhhhhhhhhhhhhhhhhhh....eeeee...hhhhhhhhhhhhhhh...eeeeeee...........eeeeehhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhh...eeeeeee...hhhhhhhh....hhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5iw8 A   3 RYDSLLQALGNTPLVGLQRLSPRWDDGRDGPHVRLWAKLEDRNPTGSIKDRPAVRMIEQAEADGLLRPGATILEPTSGNTGISLAMAARLKGYRLICVMPENTSVERRQLLELYGAQIIFSAAEGGSNTAVATAKELAATNPSWVMLYQYGNPANTDSHYCGTGPELLADLPEITHFVAGLGTTGTLMGTGRFLREHVANVKIVAAEPRYELYDPEILTARYSVGAVDAVRRTRELVHTEGIFAGISTGAVLHAALGVGAGALAAGERADIALVVADAGWKYLSTGAYAGSLDDAETAL 317
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212|      238       248       258       268       278       288       298       308         
                                                                                                                                                                                                                                           212|                                                                                        
                                                                                                                                                                                                                                            229                                                                                        


Chain B from PDB  Type:PROTEIN  Length:315
                                                                                                                                                                                                                                                                                                                                                           
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhh.....eee................eeeeeee.........hhhhhhhhhhhhhhh.......eeee..hhhhhhhhhhhhhhh..eeeeeee...hhhhh........eeeeehhhhhhhhhhhhhhhhhh....eee.....hhhhhhhhhhhhhhhhhhhh....eeeee...hhhhhhhhhhhhhhh...eeeeeee.....hhhhh.................eeeeehhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhh..eeeeeee...hhhhhhhh....hhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5iw8 B   3 RYDSLLQALGNTPLVGLQRLSPRWDDGRDGPHVRLWAKLEDRNPTGSIKDRPAVRMIEQAEADGLLRPGATILEPTSGNTGISLAMAARLKGYRLICVMPENTSVERRQLLELYGAQIIFSAAEGGSNTAVATAKELAATNPSWVMLYQYGNPANTDSHYCGTGPELLADLPEITHFVAGLGTTGTLMGTGRFLREHVANVKIVAAEPRYGEGVYALRNMDEGFVPELYDPEILTARYSVGAVDAVRRTRELVHTEGIFAGISTGAVLHAALGVGAGALAAGERADIALVVADAGWKYLSTGAYAGSLDDAETAL 317
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312
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  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 5IW8)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5IW8)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5IW8)

(-) Gene Ontology  (11, 11)

Asymmetric/Biological Unit(hide GO term definitions)

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  2.5.1.113
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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 5i7r 5iwc

(-) Related Entries Specified in the PDB File

3dki CYSM PROTEIN: LIGAND-FREE STRUCTURE
3fgp CYSM PROTEIN: LIGAND-FREE STRUCTURE