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(-) Description

Title :  CRYSTAL STRUCTURE OF M. TUBERCULOSIS DPRE1 IN COMPLEX WITH THE NON-COVALENT INHIBITOR QN114
 
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 :  2.09
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  (4, 6)

Asymmetric Unit (4, 6)
No.NameCountTypeFull Name
12J31Ligand/Ion(2R)-2-{[(2R)-2-{[(2R)-2-HYDROXYPROPYL]OXY}PROPYL]OXY}PROPAN-1-OL
2FAD2Ligand/IonFLAVIN-ADENINE DINUCLEOTIDE
3IMD1Ligand/IonIMIDAZOLE
4R582Ligand/Ion3-[(4-ETHOXYBENZYL)AMINO]-6-(TRIFLUOROMETHYL)QUINOXALINE-2-CARBOXYLIC ACID
Biological Unit 1 (4, 4)
No.NameCountTypeFull Name
12J31Ligand/Ion(2R)-2-{[(2R)-2-{[(2R)-2-HYDROXYPROPYL]OXY}PROPYL]OXY}PROPAN-1-OL
2FAD1Ligand/IonFLAVIN-ADENINE DINUCLEOTIDE
3IMD1Ligand/IonIMIDAZOLE
4R581Ligand/Ion3-[(4-ETHOXYBENZYL)AMINO]-6-(TRIFLUOROMETHYL)QUINOXALINE-2-CARBOXYLIC ACID
Biological Unit 2 (2, 2)
No.NameCountTypeFull Name
12J3-1Ligand/Ion(2R)-2-{[(2R)-2-{[(2R)-2-HYDROXYPROPYL]OXY}PROPYL]OXY}PROPAN-1-OL
2FAD1Ligand/IonFLAVIN-ADENINE DINUCLEOTIDE
3IMD-1Ligand/IonIMIDAZOLE
4R581Ligand/Ion3-[(4-ETHOXYBENZYL)AMINO]-6-(TRIFLUOROMETHYL)QUINOXALINE-2-CARBOXYLIC ACID

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
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 , R58 A:502 , HOH A:635 , HOH A:648binding site for residue FAD A 501
2AC2SOFTWARETYR A:60 , HIS A:132 , GLY A:133 , LYS A:134 , SER A:228 , GLN A:336 , VAL A:365 , LYS A:367 , CYS A:387 , LYS A:418 , FAD A:501binding site for residue R58 A 502
3AC3SOFTWAREPRO A:371 , ARG A:372 , ILE A:381 , PRO A:382 , ARG A:413 , HOH A:679 , HOH A:701binding site for residue 2J3 A 503
4AC4SOFTWARESER A:82 , ASP A:84binding site for residue IMD A 504
5AC5SOFTWARETRP 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 , R58 B:502 , HOH B:621 , HOH B:642binding site for residue FAD B 501
6AC6SOFTWARETYR B:60 , HIS B:132 , GLY B:133 , LYS B:134 , TRP B:230 , LEU B:363 , VAL B:365 , LYS B:367 , CYS B:387 , LYS B:418 , FAD B:501binding site for residue R58 B 502

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4P8M)

(-) Cis Peptide Bonds  (3, 3)

Asymmetric Unit
No.Residues
1Gly A:46 -Gly A:47
2Pro A:237 -Pro A:238
3Pro B:237 -Pro B:238

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4P8M)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4P8M)

(-) Exons   (0, 0)

(no "Exon" information available for 4P8M)

(-) 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:427
                                                                                                                                                                                                                                                                                                                                                                                                                                                                           
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee........eeeeeee..hhhhhhhhhhhhhhh.....eeee...............eeee......eeeee....eeeee...hhhhhhhhhh...ee..........hhhhhhhh.....hhhhhhhhhh.eeeeeee.....eeee.....hhhhhhhhh.......eeeeeeee.ee....eeeeeeee..hhhhhhhhhhhhhhhhh.eeeeee...........eeeeeeee.hhhhhhhhhh..........hhhhhhhhhh..eeeeeeehhhhh.........eeeeeeeee..hhhhhhhhhhhhhh........eeeee.............eeeeeeeee...hhhhhhhhhhhhhhhh..ee.hhhh...hhhhhhhhh.hhhhhhhhhhhhh......hhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4p8m A   8 TTATRLTGWGRTAPSVANVLRTPDAEMIVKAVARVAESGGGRGAIARGLGRSYGDNAQNGGGLVIDMTPLNTIHSIDADTKLVDIDAGVNLDQLMKAALPFGLWVPVLPGTRQVTVGGAIACDIHGKNHHSAGSFGNHVRSMDLLTADGEIRHLTPTGEDAELFWATVGGNGLTGIIMRATIEMTPTSTAYFIADGDVTASLDETIALHSDGSEARYTYSSAWFDAISAPPKLGRAAVSRGRLATVEQLPAKLRSEPLKFDAPGPIGELWYRKSGTYRGKVQNLTQFYHPLAYGPAGFLQYQFVIPTEAVDEFKKIIGVIQASGHYSFLNVFKLFGPRNQAPLSFPIPGWNICVDFPIKDGLGKFVSELDRRVLEFGGRLYTAKDSRTTAETFHAMYPRVDEWISVRRKVDPLRVFASDMARRLELL 461
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267  ||   296       306       316||     334       344       354       364       374       384       394       404       414       424       434       444       454       
                                                                                                                                                                                                                                                                                                270|                        317|                                                                                                                                       
                                                                                                                                                                                                                                                                                                 290                         326                                                                                                                                       


Chain B from PDB  Type:PROTEIN  Length:406
                                                                                                                                                                                                                                                                                                                                                                                                                                                      
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee........eeeeeee..hhhhhhhhhhhhhhh.....eeee...............eeee......eeeee....eeeee...hhhhhhhhhh...ee..........hhhhhhhh.....hhhhhhhhhh.eeeeeee.....eeee.....hhhhhhhhh.......eeeeeeee.ee.....eeeeeee..hhhhhhhhhhhhhhhhh.eeeeee...........eeeeeeee.hhhhhhhhhhh.......eeeeee.......eeeeeeeee..hhhhhhhhhhhhhh........eeeee.............eeeeeeeee...hhhhhhhhhhhhhhhh..ee.hhhh...hhhhhhhhh.hhhhhhhhhhhhh......hhhhhhh... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4p8m B   7 TTTATRLTGWGRTAPSVANVLRTPDAEMIVKAVARVAESGGGRGAIARGLGRSYGDNAQNGGGLVIDMTPLNTIHSIDADTKLVDIDAGVNLDQLMKAALPFGLWVPVLPGTRQVTVGGAIACDIHGKNHHSAGSFGNHVRSMDLLTADGEIRHLTPTGEDAELFWATVGGNGLTGIIMRATIEMTPTSTAYFIADGDVTASLDETIALHSDGSEARYTYSSAWFDAISAPPKLGRAAVSRGRLATVEQLPAKLRSEPLKFGTYRGKVQNLTQFAGFLQYQFVIPTEAVDEFKKIIGVIQASGHYSFLNVFKLFGPRNQAPLSFPIPGWNICVDFPIKDGLGKFVSELDRRVLEFGGRLYTAKDSRTTAETFHAMYPRVDEWISVRRKVDPLRVFASDMARRLELL 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||     309   ||  335       345       355       365       375       385       395       405       415       425       435       445       455      
                                                                                                                                                                                                                                                                                              267|         313|                                                                                                                                   
                                                                                                                                                                                                                                                                                               301          330
   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 4P8M)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4P8M)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4P8M)

(-) Gene Ontology  (14, 23)

Asymmetric Unit(hide GO term definitions)

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  4p8m
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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 4p8l 4p8n 4p8p 4p8t 4p8y
        DPRE1_MYCTU | P9WJF1: 4fdn 4fdo 4fdp 4feh 4ff6 4kw5 4ncr 4p8c 4p8h 4p8k 4p8l 4p8n 4p8p 4p8t 4p8y 4pfa 4pfd

(-) Related Entries Specified in the PDB File

4p8c 4p8h 4p8k 4p8l 4p8n 4p8p 4p8t 4p8y