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(-) Description

Title :  BIANTHRANILATE-LIKE INHIBITOR WITH 6 ATOM "LINE" AND PHOSPHONATE "HOOK" FISHING FOR HYDROGEN BOND DONORS IN MYCOBACTERIUM TUBERCULOSIS ANTHRANILATE PHOSPHORIBOSYLTRANSFERASE (ANPRT; TRPD)
 
Authors :  G. L. Evans, E. N. Baker, J. S. Lott, Tb Structural Genomics Consorti (Tbsgc)
Date :  06 May 15  (Deposition) - 25 May 16  (Release) - 25 May 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.15
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
Keywords :  Inhibitor, Complex, Lobenzarit-Like Analogue, Trpd, Anprt, Tb Structural Genomics Consortium, Tbsgc, Phosphoribosyltransferase, Magnesium Binding, Phosphoribosylpyrophosphate, Prpp, Transferase- Transferase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  G. L. Evans, E. N. Baker, J. S. Lott
Binding And Mimicking Of The Phosphate-Rich Substrate, Prpp
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - ANTHRANILATE PHOSPHORIBOSYLTRANSFERASE
    Chains: A, B, C, D
    EC Number: 2.4.2.18
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET23A
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: TRPD, RV2192C, MTCY190.03C
    Organism Scientific: MYCOBACTERIUM TUBERCULOSIS
    Organism Taxid: 83332
    Strain: ATCC 25618 / H37RV

 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, 7)

Asymmetric Unit (2, 7)
No.NameCountTypeFull Name
17P33Ligand/Ion2-[(2-CARBOXYPHENYL)AMINO]-5-[(5-PHOSPHONOPENTYL)OXY]BENZOIC ACID
2IMD4Ligand/IonIMIDAZOLE
Biological Unit 1 (2, 5)
No.NameCountTypeFull Name
17P32Ligand/Ion2-[(2-CARBOXYPHENYL)AMINO]-5-[(5-PHOSPHONOPENTYL)OXY]BENZOIC ACID
2IMD3Ligand/IonIMIDAZOLE
Biological Unit 2 (2, 2)
No.NameCountTypeFull Name
17P31Ligand/Ion2-[(2-CARBOXYPHENYL)AMINO]-5-[(5-PHOSPHONOPENTYL)OXY]BENZOIC ACID
2IMD1Ligand/IonIMIDAZOLE

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREMET A:86 , HIS A:136 , GLY A:137 , ASN A:138 , ALA A:179 , PRO A:180 , HIS A:183 , TYR A:186 , ARG A:187 , ALA A:190 , ARG A:193 , ARG A:194 , HOH A:517 , HOH A:518 , HOH A:535 , HOH A:594binding site for residue 7P3 A 400
2AC2SOFTWARELEU A:305 , GLY A:306 , GLY A:307 , ILE A:351 , ASP A:352 , GLU A:357 , ALA D:236 , ARG D:237 , ARG D:238binding site for residue IMD A 401
3AC3SOFTWAREASN B:138 , ALA B:179 , PRO B:180 , HIS B:183 , TYR B:186 , ARG B:187 , ALA B:190 , ARG B:194 , IMD B:402binding site for residue 7P3 B 400
4AC4SOFTWAREASP B:159 , ARG B:181 , IMD B:402binding site for residue IMD B 401
5AC5SOFTWARE7P3 B:400 , IMD B:401binding site for residue IMD B 402
6AC6SOFTWARELEU B:305 , GLY B:306 , GLY B:307 , ILE B:351 , GLU B:357 , ARG C:213binding site for residue IMD C 400
7AC7SOFTWAREMET D:86 , HIS D:136 , ASN D:138 , ALA D:179 , PRO D:180 , HIS D:183 , TYR D:186 , ARG D:187 , ALA D:190 , ARG D:193 , ARG D:194 , HOH D:514 , HOH D:555binding site for residue 7P3 D 400

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5BNE)

(-) 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:335
                                                                                                                                                                                                                                                                                                                                                                               
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhh......hhhhhhhhhhhh...hhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhh............eeeee.....hhhhhhhhhhhhhh...eeeee....hhhhhhhh......hhhhhhhhhhhhheeeeehhhhh..hhhhhhhhhhhh..hhhhhhhhhh......eeeee..hhhhhhhhhhhhhhh..eeeeeee............eeeeeee..eeeeeeehhhhhh....hhhhh.hhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5bne A  25 PSWPQILGRLTDNRDLARGQAAWAMDQIMTGNARPAQIAAFAVAMTMKAPTADEVGELAGVMLSHAHPLPADTVPDDAVDVVGTGGDTVNLSTMAAIVVAAAGVPVVKHGNRAGGADTLEALGVRIDLGPDLVARSLAEVGIGFCFAPRFHPSYRHAAAVRREIGVPTVFNLLGPLTNPARPRAGLIGCAFADLAEVMAGVFAARRSSVLVVHGDDGLDELTTTTTSTIWRVAAGSVDKLTFDPAGFGFARAQLDQLGDAQANAAAVRAVLGGARGPVRDAVVLNAAGAIVAHAGLSSRAEWLPAWEEGLRRASAAIDTGAAEQLLARWVRFGRQ 369
                                    34        44        54        64        74        84        94       104      |117       127       137  ||   152       162       172       182       192       202       212       222       232       242       252       262       272       282      |294       304       314       324       334       344       354       364     
                                                                                                                111|                      140|                                                                                                                                            289|                                                                             
                                                                                                                 115                       146                                                                                                                                             292                                                                             


Chain B from PDB  Type:PROTEIN  Length:331
                                                                                                                                                                                                                                                                                                                                                                           
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhh......hhhhhhhhhhhh...hhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhh.............eeeee...hhhhhhhhhhhh...eeeee.....hhhhhh......hhhhhhhhhhhh.eeeeehhhhh..hhhhhhhhhhhh..hhhhhhhhhh......eeeee..hhhhhhhhhhhhhhh..eeeeeee............eeeeeee..eeeeeeehhhhhh...........hhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5bne B  25 PSWPQILGRLTDNRDLARGQAAWAMDQIMTGNARPAQIAAFAVAMTMKAPTADEVGELAGVMLSHAHPLPADTVPDDAVDVVGTGNLSTMAAIVVAAAGVPVVKHGNRAAADTLEALGVRIDLGPDLVARSLAEVGIGFCFAPRFHPSYRHAAAVRREIGVPTVFNLLGPLTNPARPRAGLIGCAFADLAEVMAGVFAARRSSVLVVHGDDGLDELTTTTTSTIWRVAAGSVDKLTFDPAGFGFARAQLDQLAGDAQANAAAVRAVLGGARGPVRDAVVLNAAGAIVAHAGLSSRAEWLPAWEEGLRRASAAIDTGAAEQLLARWVRFGRQ 369
                                    34        44        54        64        74        84        94       104    || 121       131       141|      157       167       177       187       197       207       217       227       237       247       257       267       277       287  ||   298       308       318       328       338       348       358       368 
                                                                                                              109|                     141|                                                                                                                                           290|                                                                             
                                                                                                               117                      148                                                                                                                                            292                                                                             


Chain C from PDB  Type:PROTEIN  Length:333
                                                                                                                                                                                                                                                                                                                                                                             
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhh......hhhhhhhhhhhh...hhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhh.............eeeee..hhhhhhhhhhhhh...eeeee....hhhhhhhhh.....hhhhhhhhhhhh.eeeeehhhhh..hhhhhhhhhhhh..hhhhhhhhhh......eeeee..hhhhhhhhhhhhhhh..eeeeeee............eeeeeee..eeeeeeehhhhhh....hhhhh...hhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5bne C  25 PSWPQILGRLTDNRDLARGQAAWAMDQIMTGNARPAQIAAFAVAMTMKAPTADEVGELAGVMLSHAHPLPADTVPDDAVDVVGTVNLSTMAAIVVAAAGVPVVKHGNRAGGADTLEALGVRIDLGPDLVARSLAEVGIGFCFAPRFHPSYRHAAAVRREIGVPTVFNLLGPLTNPARPRAGLIGCAFADLAEVMAGVFAARRSSVLVVHGDDGLDELTTTTTSTIWRVAAGSVDKLTFDPAGFGFARAQLDQLAGGDAQANAAAVRAVLGGARGPVRDAVVLNAAGAIVAHAGLSSRAEWLPAWEEGLRRASAAIDTGAAEQLLARWVRFGRQ 369
                                    34        44        54        64        74        84        94       104   ||  121       131       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       356       366   
                                                                                                             108|                     140|                                                                                                                                                                                                                               
                                                                                                              116                      146                                                                                                                                                                                                                               


Chain D from PDB  Type:PROTEIN  Length:327
                                                                                                                                                                                                                                                                                                                                                                       
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhh......hhhhhhhhhhhh...hhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhh.............eeeee....hhhhhhhhhhhh...eeeee....hhhhhhhh.....hhhhhhhhhhhhheeeeehhhhh..hhhhhhhhhhhh..hhhhhhhhhh......eeeee..hhhhhhhhhhhhhhh..eeeeeee............eeeeeee..eeeeeeehhhhhh.........hhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5bne D  25 PSWPQILGRLTDNRDLARGQAAWAMDQIMTGNARPAQIAAFAVAMTMKAPTADEVGELAGVMLSHAHPLPADTVPDDAVDVVGTGGNLSTMAAIVVAAAGVPVVKHGNRAGADTLEALGVRIDLGPDLVARSLAEVGIGFCFAPRFHPSYRHAAAVRREIGVPTVFNLLGPLTNPARPRAGLIGCAFADLAEVMAGVFAARRSSVLVVHGDDGLDELTTTTTSTIWRVAAGSVDKLTFDPAGFGFARAQLDDAQANAAAVRAVLGGARGPVRDAVVLNAAGAIVAHAGLSSAEWLPAWEEGLRRASAAIDTGAAEQLLARWVRFGRQ 369
                                    34        44        54        64        74        84        94       104     ||120       130       140|      156       166       176       186       196       206       216       226       236       246       256       266       276       286||     301       311       321       331||     342       352       362       
                                                                                                               110|                    140|                                                                                                                                         287|                                    332|                                   
                                                                                                                117                     147                                                                                                                                          293                                     334
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → 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 5BNE)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (14, 14)

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  2.4.2.18
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 Related Entries

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

UniProtKB/Swiss-Prot
        TRPD_MYCTU | P9WFX5: 1zvw 2bpq 3qqs 3qr9 3qs8 3qsa 3r6c 3r88 3twp 3uu1 4giu 4gkm 4ij1 4m0r 4n5v 4n8q 4n93 4owm 4own 4owo 4owq 4ows 4owu 4owv 4x58 4x59 4x5a 4x5b 4x5c 4x5d 4x5e 5byt 5c1r 5c2l 5c7s

(-) Related Entries Specified in the PDB File

3qr9 3QR9 CONTAINS THE SAME PROTEIN WITH NO LIGANDS BOUND AND WAS USED IN MR FOR THIS STRUCTURE
4ij1 4IJ1 CONTAINS THE PARENT INHIBITOR (I.E. WITHOUT PHOSPHONATE " FISHING LINE") BOUND TO THE SAME PROTEIN