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(-) Description

Title :  CRYSTAL STRUCTURE OF M. TUBERCULOSIS DPRE1 IN COMPLEX WITH THE NON-COVALENT INHIBITOR TY21C
 
Authors :  J. Neres, F. Pojer, S. T. Cole
Date :  01 Apr 14  (Deposition) - 10 Dec 14  (Release) - 01 Apr 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.01
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, 4)

Asymmetric Unit (3, 4)
No.NameCountTypeFull Name
138C1Ligand/Ion3-[(4-METHOXYBENZYL)AMINO]-6-(TRIFLUOROMETHYL)QUINOXALINE-2-CARBOXYLIC ACID
2FAD2Ligand/IonFLAVIN-ADENINE DINUCLEOTIDE
3IMD1Ligand/IonIMIDAZOLE
Biological Unit 1 (3, 3)
No.NameCountTypeFull Name
138C1Ligand/Ion3-[(4-METHOXYBENZYL)AMINO]-6-(TRIFLUOROMETHYL)QUINOXALINE-2-CARBOXYLIC ACID
2FAD1Ligand/IonFLAVIN-ADENINE DINUCLEOTIDE
3IMD1Ligand/IonIMIDAZOLE
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
138C-1Ligand/Ion3-[(4-METHOXYBENZYL)AMINO]-6-(TRIFLUOROMETHYL)QUINOXALINE-2-CARBOXYLIC ACID
2FAD1Ligand/IonFLAVIN-ADENINE DINUCLEOTIDE
3IMD-1Ligand/IonIMIDAZOLE

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
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 , 38C A:502 , HOH A:664 , HOH A:677binding site for residue FAD A 501
2AC2SOFTWARETYR A:60 , HIS A:132 , GLY A:133 , LYS A:134 , ASN A:324 , ARG A:325 , GLN A:334 , GLN A:336 , VAL A:365 , LYS A:367 , ASN A:385 , CYS A:387 , LYS A:418 , FAD A:501binding site for residue 38C 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 , ARG B:54 , 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 , HOH B:639 , HOH B:642binding site for residue FAD B 501

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4P8Y)

(-) Cis Peptide Bonds  (3, 3)

Asymmetric Unit
No.Residues
1Ser A:45 -Gly A:46
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 4P8Y)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4P8Y)

(-) Exons   (0, 0)

(no "Exon" information available for 4P8Y)

(-) 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:455
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeee........eeeeeee..hhhhhhhhhhhhhhh.....eeee...............eeee......eeeee....eeeee...hhhhhhhhhh...ee..........hhhhhhhh.....hhhhhhhhhh.eeeeeee.....eeee.....hhhhhhhhh.......eeeeeeee.ee.....eeeeeee..hhhhhhhhhhhhhhhhh.eeeeee...........eeeeeeee.hhhhhhhhhh............hhhhhh..........hhhhhhhhhhhh.eeeeeehhhhhhhhhhhhhhhh....eeeeeeeee..hhhhhhhhhhhhhh........eeeee.............eeeeeeeee...hhhhhhhhhhhhhhhh..ee........hhhhhhhhh.hhhhhhhhhhhhh......hhhhhhh... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4p8y A   4 VGATTTATRLTGWGRTAPSVANVLRTPDAEMIVKAVARVAESGGGRGAIARGLGRSYGDNAQNGGGLVIDMTPLNTIHSIDADTKLVDIDAGVNLDQLMKAALPFGLWVPVLPGTRQVTVGGAIACDIHGKNHHSAGSFGNHVRSMDLLTADGEIRHLTPTGEDAELFWATVGGNGLTGIIMRATIEMTPTSTAYFIADGDVTASLDETIALHSDGSEARYTYSSAWFDAISAPPKLGRAAVSRGRLATVEQLPAKLRSEPLKFDAPQLLTLPDVFPNGLANKYTFGPIGELWYRKSGTYRGKVQNLTQFYHPLDMFGEWNRAAGFLQYQFVIPTEAVDEFKKIIGVIQASGHYSFLNVFKLFGPRNQAPLSFPIPGWNICVDFPIKDGLGKFVSELDRRVLEFGGRLYTAKDSRTTAETFHAMYPRVDEWISVRRKVDPLRVFASDMARRLELL 461
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323  ||   336       346       356       366       376       386       396       406       416       426       436       446       456     
                                                                                                                                                                                                                                                                                                                                                            326|                                                                                                                                   
                                                                                                                                                                                                                                                                                                                                                             330                                                                                                                                   


Chain B from PDB  Type:PROTEIN  Length:416
                                                                                                                                                                                                                                                                                                                                                                                                                                                                
               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.....eeeeeee..hhhhhhhhhhhhhhhhh.eeeeee...........eeeeeeee.hhhhhhhhhhh.........hhhhhhh.eeeeeehhhhhh.eeeeeeeee..hhhhhhhhhhhhhhh.......eeeee.............eeeeeeeee...hhhhhhhhhhhhhhhh..ee........hhhhhhhhh.hhhhhhhhhhhhh......hhhhhhh... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4p8y B   7 TTTATRLTGWGRTAPSVANVLRTPDAEMIVKAVARVAESGGGRGAIARGLGRSYGDNAQNGGGLVIDMTPLNTIHSIDADTKLVDIDAGVNLDQLMKAALPFGLWVPVLPGTRQVTVGGAIACDIHGKNHHSAGSFGNHVRSMDLLTADGEIRHLTPTGEDAELFWATVGGNGLTGIIMRATIEMTPTSTAYFIADGDVTASLDETIALHSDGSEARYTYSSAWFDAISAPPKLGRAAVSRGRLATVEQLPAKLRSEPLKFDAPELWYRKSGTYRGKVQNLTQFYGFLQYQFVIPTEAVDEFKKIIGVIQASGHYSFLNVFKLFGPRNQAPLSFPIPGWNICVDFPIKDGLGKFVSELDRRVLEFGGRLYTAKDSRTTAETFHAMYPRVDEWISVRRKVDPLRVFASDMARRLELL 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   ||  299       309    || 335       345       355       365       375       385       395       405       415       425       435       445       455      
                                                                                                                                                                                                                                                                                                 270|                 314|                                                                                                                                  
                                                                                                                                                                                                                                                                                                  294                  331
   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 4P8Y)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4P8Y)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4P8Y)

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

(-) Related Entries Specified in the PDB File

4p8c 4p8h 4p8k 4p8l 4p8m 4p8n 4p8p 4p8t