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(-) Description

Title :  CRYSTAL STRUCTURE OF M. TUBERCULOSIS DPRE1 IN COMPLEX WITH THE NON-COVALENT INHIBITOR TY36C
 
Authors :  J. Neres, F. Pojer, S. T. Cole
Date :  31 Mar 14  (Deposition) - 10 Dec 14  (Release) - 01 Apr 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.02
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Dpre1, Inhibitor, Complex, Non-Covalent, Oxidoreductase- Oxidoreductase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. Neres, R. C. Hartkoorn, L. R. Chiarelli, R. Gadupudi, M. R. Pasca, G. Mori, A. Venturelli, S. Savina, V. Makarov, G. S. Kolly, E. Molteni, C. Binda, N. Dhar, S. Ferrari, P. Brodin, V. Delorme, V. Landry, A. L. De Jesus Lopes Ribeiro, D. Farina, P. Saxena, F. Pojer, A. Carta, R. Luciani, A. Porta, G. Zanoni, E. De Rossi, M. P. Costi, G. Riccardi, S. T. Cole
2-Carboxyquinoxalines Kill Mycobacterium Tuberculosis Through Noncovalent Inhibition Of Dpre1.
Acs Chem. Biol. V. 10 705 2015
PubMed-ID: 25427196  |  Reference-DOI: 10.1021/CB5007163

(-) Compounds

Molecule 1 - PROBABLE DECAPRENYLPHOSPHORYL-BETA-D-RIBOSE OXIDASE
    Chains: A, B
    EC Number: 1.-.-.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET28B
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: DPRE1, RV3790, MT3898
    Organism Scientific: MYCOBACTERIUM TUBERCULOSIS
    Organism Taxid: 83332
    Strain: H37RV
    Synonym: DPRE1

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): A 
Biological Unit 2 (1x):  B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 5)

Asymmetric Unit (3, 5)
No.NameCountTypeFull Name
136C2Ligand/Ion3-[(4-FLUOROBENZYL)AMINO]-6-(TRIFLUOROMETHYL)QUINOXALINE-2-CARBOXYLIC ACID
2FAD2Ligand/IonFLAVIN-ADENINE DINUCLEOTIDE
3IMD1Ligand/IonIMIDAZOLE
Biological Unit 1 (3, 3)
No.NameCountTypeFull Name
136C1Ligand/Ion3-[(4-FLUOROBENZYL)AMINO]-6-(TRIFLUOROMETHYL)QUINOXALINE-2-CARBOXYLIC ACID
2FAD1Ligand/IonFLAVIN-ADENINE DINUCLEOTIDE
3IMD1Ligand/IonIMIDAZOLE
Biological Unit 2 (2, 2)
No.NameCountTypeFull Name
136C1Ligand/Ion3-[(4-FLUOROBENZYL)AMINO]-6-(TRIFLUOROMETHYL)QUINOXALINE-2-CARBOXYLIC ACID
2FAD1Ligand/IonFLAVIN-ADENINE DINUCLEOTIDE
3IMD-1Ligand/IonIMIDAZOLE

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETRP A:16 , ILE A:52 , ALA A:53 , GLY A:55 , LEU A:56 , GLY A:57 , ARG A:58 , SER A:59 , TYR A:60 , ASN A:63 , ALA A:64 , MET A:74 , ALA A:94 , PRO A:116 , GLY A:117 , THR A:118 , VAL A:121 , THR A:122 , GLY A:124 , GLY A:125 , ALA A:128 , CYS A:129 , ILE A:131 , HIS A:132 , ASN A:178 , GLY A:179 , GLY A:182 , ILE A:184 , TYR A:415 , ALA A:417 , 36C A:502 , HOH A:658 , HOH A:660binding site for residue FAD A 501
2AC2SOFTWARETYR A:60 , HIS A:132 , GLY A:133 , LYS A:134 , LEU A:317 , ASN A:324 , ARG A:325 , GLN A:336 , VAL A:365 , LYS A:367 , ASN A:385 , CYS A:387 , LYS A:418 , FAD A:501binding site for residue 36C A 502
3AC3SOFTWARESER A:82 , ASP A:84 , SER B:82 , ASP B:84binding site for residue IMD A 503
4AC4SOFTWARETRP B:16 , ILE B:52 , ALA B:53 , GLY B:55 , LEU B:56 , GLY B:57 , ARG B:58 , SER B:59 , TYR B:60 , ASN B:63 , ALA B:64 , MET B:74 , ALA B:94 , PRO B:116 , GLY B:117 , THR B:118 , VAL B:121 , THR B:122 , GLY B:124 , GLY B:125 , ALA B:128 , CYS B:129 , ILE B:131 , HIS B:132 , ASN B:178 , GLY B:179 , GLY B:182 , ILE B:184 , TYR B:415 , ALA B:417 , 36C B:502 , HOH B:623 , HOH B:650binding site for residue FAD B 501
5AC5SOFTWARETYR B:60 , HIS B:132 , GLY B:133 , LYS B:134 , TRP B:230 , ASN B:364 , VAL B:365 , LYS B:367 , CYS B:387 , LYS B:418 , FAD B:501binding site for residue 36C B 502

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4P8L)

(-) Cis Peptide Bonds  (5, 5)

Asymmetric Unit
No.Residues
1Ser A:45 -Gly A:46
2Pro A:237 -Pro A:238
3Gly B:48 -Arg B:49
4Pro B:237 -Pro B:238
5His B:315 -Pro B:316

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4P8L)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4P8L)

(-) Exons   (0, 0)

(no "Exon" information available for 4P8L)

(-) 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:457
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeee........eeeeeee..hhhhhhhhhhhhhhhh....eeee...............eeee......eeeee....eeeee...hhhhhhhhhh...ee..........hhhhhhhh.....hhhhhhhhhh.eeeeeee.....eeee.....hhhhhhhhh.......eeeeeeee.ee.....eeeeeee..hhhhhhhhhhhhhhhhh.eeeeee...........eeeeeeee.hhhhhhhhhhh...........hhhhhh..........hhhhhhhhhhhh.eeeeeehhhhhhhhhhhhhhhh.......eeeeeeeee..hhhhhhhhhhhhhhh.......eeeee.............eeeeeeeee...hhhhhhhhhhhhhhhh..ee........hhhhhhhhh.hhhhhhhhhhhhh......hhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4p8l A   5 GATTTATRLTGWGRTAPSVANVLRTPDAEMIVKAVARVAESGGGRGAIARGLGRSYGDNAQNGGGLVIDMTPLNTIHSIDADTKLVDIDAGVNLDQLMKAALPFGLWVPVLPGTRQVTVGGAIACDIHGKNHHSAGSFGNHVRSMDLLTADGEIRHLTPTGEDAELFWATVGGNGLTGIIMRATIEMTPTSTAYFIADGDVTASLDETIALHSDGSEARYTYSSAWFDAISAPPKLGRAAVSRGRLATVEQLPAKLRSEPLKFDAPQLLTLPDVFPNGLANKYTFGPIGELWYRKSGTYRGKVQNLTQFYHPLDMFGEWNRAYGPAGFLQYQFVIPTEAVDEFKKIIGVIQASGHYSFLNVFKLFGPRNQAPLSFPIPGWNICVDFPIKDGLGKFVSELDRRVLEFGGRLYTAKDSRTTAETFHAMYPRVDEWISVRRKVDPLRVFASDMARRLELL 461
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404       414       424       434       444       454       


Chain B from PDB  Type:PROTEIN  Length:419
                                                                                                                                                                                                                                                                                                                                                                                                                                                                   
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee........eeeeee...hhhhhhhhhhhhhhhh....eeee...............eeee......eeeee....eeeee...hhhhhhhhhh...ee..........hhhhhhhh.....hhhhhhhhhh.eeeeeee.....eeee.....hhhhhhhhh.......eeeeeeee.ee.....eeeeeee..hhhhhhhhhhhhhhhhh.eeeeee...........eeeeeeee.hhhhhhhhhhh.........hhhhhhhh.eeeeeehhhhhh...eeeeeeeee..hhhhhhhhhhhhhhh.......eeeee.............eeeeeeeee...hhhhhhhhhhhhhhhh..ee........hhhhhhhhh.hhhhhhhhhhhhh......hhhhhhh... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4p8l B   7 TTTATRLTGWGRTAPSVANVLRTPDAEMIVKAVARVAESGGGRGAIARGLGRSYGDNAQNGGGLVIDMTPLNTIHSIDADTKLVDIDAGVNLDQLMKAALPFGLWVPVLPGTRQVTVGGAIACDIHGKNHHSAGSFGNHVRSMDLLTADGEIRHLTPTGEDAELFWATVGGNGLTGIIMRATIEMTPTSTAYFIADGDVTASLDETIALHSDGSEARYTYSSAWFDAISAPPKLGRAAVSRGRLATVEQLPAKLRSEPLKFDAPGELWYRKSGTYRGKVQNLTQFYHPGFLQYQFVIPTEAVDEFKKIIGVIQASGHYSFLNVFKLFGPRNQAPLSFPIPGWNICVDFPIKDGLGKFVSELDRRVLEFGGRLYTAKDSRTTAETFHAMYPRVDEWISVRRKVDPLRVFASDMARRLELL 461
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266   ||  298       308       332       342       352       362       372       382       392       402       412       422       432       442       452         
                                                                                                                                                                                                                                                                                                 270|                    316|                                                                                                                                  
                                                                                                                                                                                                                                                                                                  293                     331
   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 4P8L)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4P8L)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4P8L)

(-) Gene Ontology  (14, 23)

Asymmetric Unit(hide GO term definitions)

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 Related Entries

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

UniProtKB/Swiss-Prot
        DPRE1_MYCTO | P9WJF0: 4fdn 4fdo 4fdp 4feh 4ff6 4ncr 4p8c 4p8h 4p8k 4p8m 4p8n 4p8p 4p8t 4p8y
        DPRE1_MYCTU | P9WJF1: 4fdn 4fdo 4fdp 4feh 4ff6 4kw5 4ncr 4p8c 4p8h 4p8k 4p8m 4p8n 4p8p 4p8t 4p8y 4pfa 4pfd

(-) Related Entries Specified in the PDB File

4p8c 4p8h 4p8k 4p8m 4p8n 4p8p 4p8t 4p8y