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(-) Description

Title :  CRYSTAL STRUCTURE OF M. TUBERCULOSIS IN COMPLEX WITH A CBT - NON-COVALENT ADDUCT
 
Authors :  J. Neres, M. Panda, S. Cole
Date :  28 Apr 14  (Deposition) - 21 Oct 15  (Release) - 21 Oct 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Dpre1, Inhibitor, Covalent, Oxidoreductase-Oxidoreductase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. Neres, S. Cole
Crystal Structure Of M. Tuberculosis In Complex With A Cbt
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - PROBABLE DECAPRENYLPHOSPHORYL-BETA-D-RIBOSE OXIDASE
    Chains: A, B
    EC Number: 1.-.-.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Cell Line: BL21(DE3)
    Expression System Plasmid: PET28A
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: DPRE1, RV3790
    Organism Scientific: MYCOBACTERIUM TUBERCULOSIS
    Organism Taxid: 83332
    Strain: ATCC 25618 / H37RV

 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, 6)

Asymmetric Unit (3, 6)
No.NameCountTypeFull Name
12R22Ligand/Ion[4-(2-METHOXYETHYL)PIPERAZIN-1-YL][6-METHYL-7-NITRO-5-(TRIFLUOROMETHYL)-1,3-BENZOTHIAZOL-2-YL]METHANONE
2FAD2Ligand/IonFLAVIN-ADENINE DINUCLEOTIDE
3IMD2Ligand/IonIMIDAZOLE
Biological Unit 1 (3, 3)
No.NameCountTypeFull Name
12R21Ligand/Ion[4-(2-METHOXYETHYL)PIPERAZIN-1-YL][6-METHYL-7-NITRO-5-(TRIFLUOROMETHYL)-1,3-BENZOTHIAZOL-2-YL]METHANONE
2FAD1Ligand/IonFLAVIN-ADENINE DINUCLEOTIDE
3IMD1Ligand/IonIMIDAZOLE
Biological Unit 2 (3, 3)
No.NameCountTypeFull Name
12R21Ligand/Ion[4-(2-METHOXYETHYL)PIPERAZIN-1-YL][6-METHYL-7-NITRO-5-(TRIFLUOROMETHYL)-1,3-BENZOTHIAZOL-2-YL]METHANONE
2FAD1Ligand/IonFLAVIN-ADENINE DINUCLEOTIDE
3IMD1Ligand/IonIMIDAZOLE

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETRP A:16 , ILE A:52 , ALA A:53 , ARG A:54 , 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 , 2R2 A:503 , HOH A:620 , HOH A:658binding site for residue FAD A 501
2AC2SOFTWARESER A:82 , ASP A:84binding site for residue IMD A 502
3AC3SOFTWARETYR A:60 , GLY A:117 , HIS A:132 , LYS A:134 , SER A:228 , TYR A:314 , LEU A:317 , GLN A:334 , GLN A:336 , LEU A:363 , VAL A:365 , ASN A:385 , LYS A:418 , FAD A:501binding site for residue 2R2 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 , 2R2 B:502 , HOH B:627 , HOH B:636binding site for residue FAD B 501
5AC5SOFTWARETYR B:60 , GLY B:117 , HIS B:132 , LYS B:134 , SER B:228 , TYR B:314 , GLN B:336 , VAL B:365 , ASN B:385 , CYS B:387 , ASP B:389 , LYS B:418 , FAD B:501binding site for residue 2R2 B 502
6AC6SOFTWAREPRO B:116 , GLY B:117 , ARG B:119 , LEU B:310binding site for residue IMD B 503

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (4, 4)

Asymmetric Unit
No.Residues
1Pro A:237 -Pro A:238
2His A:315 -Pro A:316
3Gly B:47 -Gly B:48
4Pro B:237 -Pro B:238

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4PFD)

(-) 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......eeee.....eeeee...hhhhhhhhhh...ee..........hhhhhhhh.....hhhhhhhhhh.eeeeeee.....eeee.....hhhhhhhhh.......eeeeeeee.ee....eeeeeeee..hhhhhhhhhhhhhhhhh.eeeeee...........eeeeeeee.hhhhhhhhhhh......hhhhhhhhhh..eeeeeeehhhhhh..........eeeeeeeee..hhhhhhhhhhhhhh........eeeee.............eeeeeeeee...hhhhhhhhhhhhhhhh..ee.hhhh...hhhhhhhhh.hhhhhhhhhhhhh......hhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4pfd A   7 TTTATRLTGWGRTAPSVANVLRTPDAEMIVKAVARVAESGGGRGAIARGLGRSYGDNAQNGGGLVIDMTPLNTIHSIDADTKLVDIDAGVNLDQLMKAALPFGLWVPVLPGTRQVTVGGAIACDIHGKNHHSAGSFGNHVRSMDLLTADGEIRHLTPTGEDAELFWATVGGNGLTGIIMRATIEMTPTSTAYFIADGDVTASLDETIALHSDGSEARYTYSSAWFDAISAPPKLGRAAVSRGRLATVEQLPAKLRSEPLKFGPIGELWYRKSGTYRGKVQNLTQFYHPLDMAYGPAGFLQYQFVIPTEAVDEFKKIIGVIQASGHYSFLNVFKLFGPRNQAPLSFPIPGWNICVDFPIKDGLGKFVSELDRRVLEFGGRLYTAKDSRTTAETFHAMYPRVDEWISVRRKVDPLRVFASDMARRLELL 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       318||     334       344       354       364       374       384       394       404       414       424       434       444       454       
                                                                                                                                                                                                                                                                                              267|                          319|                                                                                                                                       
                                                                                                                                                                                                                                                                                               290                           326                                                                                                                                       


Chain B from PDB  Type:PROTEIN  Length:410
                                                                                                                                                                                                                                                                                                                                                                                                                                                          
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee........eeeeee...hhhhhhhhhhhhhhh.....eeee...............eeee......eeee.....eeeee...hhhhhhhhhh...ee..........hhhhhhhh.....hhhhhhhhhh.eeeeeee.....eeee.....hhhhhhhhh.......eeeeeeee.ee....eeeeeeee..hhhhhhhhhhhhhhhhh.eeeeee...........eeeeeeee.hhhhhhhhhhh.........eeeeeeehhhhhh..eeeeeeeee..hhhhhhhhhhhhhhh.......eeeee.............eeeeeeeee...hhhhhhhhhhhhhhhh..ee.hhhh...hhhhhhhhh.hhhhhhhhhhhhh......hhhhhhh... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4pfd B   7 TTTATRLTGWGRTAPSVANVLRTPDAEMIVKAVARVAESGGGRGAIARGLGRSYGDNAQNGGGLVIDMTPLNTIHSIDADTKLVDIDAGVNLDQLMKAALPFGLWVPVLPGTRQVTVGGAIACDIHGKNHHSAGSFGNHVRSMDLLTADGEIRHLTPTGEDAELFWATVGGNGLTGIIMRATIEMTPTSTAYFIADGDVTASLDETIALHSDGSEARYTYSSAWFDAISAPPKLGRAAVSRGRLATVEQLPAKLRSEPLKFKSGTYRGKVQNLTQFYHAGFLQYQFVIPTEAVDEFKKIIGVIQASGHYSFLNVFKLFGPRNQAPLSFPIPGWNICVDFPIKDGLGKFVSELDRRVLEFGGRLYTAKDSRTTAETFHAMYPRVDEWISVRRKVDPLRVFASDMARRLELL 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||     307       331       341       351       361       371       381       391       401       411       421       431       441       451       461
                                                                                                                                                                                                                                                                                              267|             315|                                                                                                                                   
                                                                                                                                                                                                                                                                                               299              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 4PFD)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (14, 14)

Asymmetric Unit(hide GO term definitions)

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  4pfd
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 Related Entries

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

UniProtKB/Swiss-Prot
        DPRE1_MYCTU | P9WJF1: 4fdn 4fdo 4fdp 4feh 4ff6 4kw5 4ncr 4p8c 4p8h 4p8k 4p8l 4p8m 4p8n 4p8p 4p8t 4p8y 4pfa

(-) Related Entries Specified in the PDB File

4p8h 4pfa