Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asymmetric Unit
(-)Asym. Unit - sites
(-)Biological Unit 1
(-)Biol. Unit 1 - sites
(-)Biological Unit 2
collapse expand < >
Image Asymmetric Unit
Asymmetric Unit  (Jmol Viewer)
Image Asym. Unit - sites
Asym. Unit - sites  (Jmol Viewer)
Image Biological Unit 1
Biological Unit 1  (Jmol Viewer)
Image Biol. Unit 1 - sites
Biol. Unit 1 - sites  (Jmol Viewer)
Image Biological Unit 2
Biological Unit 2  (Jmol Viewer)

(-) Description

Title :  MYCOBACTERIUM TUBERCULOSIS DPRE1 IN COMPLEX WITH CT325 - MONOCLINIC CRYSTAL FORM
 
Authors :  S. M. Batt, G. S. Besra, K. Futterer
Date :  31 May 12  (Deposition) - 04 Jul 12  (Release) - 31 Oct 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.60
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Alpha+Beta, Oxidoreductase, Decaprenylphosphoryl-Beta-D-Ribose, Oxidoreductase-Oxidoreductase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. M. Batt, T. Jabeen, V. Bhowruth, L. Quill, P. A. Lund, L. Eggeling, L. J. Alderwick, K. Futterer, G. S. Besra
Structural Basis Of Inhibition Of Mycobacterium Tuberculosi Dpre1 By Benzothiazinone Inhibitors.
Proc. Natl. Acad. Sci. Usa V. 109 11354 2012
PubMed-ID: 22733761  |  Reference-DOI: 10.1073/PNAS.1205735109

(-) Compounds

Molecule 1 - PROBABLE DECAPRENYLPHOSPHORYL-BETA-D-RIBOSE OXIDASE
    Chains: A, B
    EC Number: 1.-.-.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET28A
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: DPRE1, MT3898, RV3790
    Organism Scientific: MYCOBACTERIUM TUBERCULOSIS
    Organism Taxid: 1773
    Strain: 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, 7)

Asymmetric Unit (3, 7)
No.NameCountTypeFull Name
10T42Ligand/Ion3-(HYDROXYAMINO)-N-[(1R)-1-PHENYLETHYL]-5-(TRIFLUOROMETHYL)BENZAMIDE
2FAD2Ligand/IonFLAVIN-ADENINE DINUCLEOTIDE
3IMD3Ligand/IonIMIDAZOLE
Biological Unit 1 (3, 4)
No.NameCountTypeFull Name
10T41Ligand/Ion3-(HYDROXYAMINO)-N-[(1R)-1-PHENYLETHYL]-5-(TRIFLUOROMETHYL)BENZAMIDE
2FAD1Ligand/IonFLAVIN-ADENINE DINUCLEOTIDE
3IMD2Ligand/IonIMIDAZOLE
Biological Unit 2 (3, 3)
No.NameCountTypeFull Name
10T41Ligand/Ion3-(HYDROXYAMINO)-N-[(1R)-1-PHENYLETHYL]-5-(TRIFLUOROMETHYL)BENZAMIDE
2FAD1Ligand/IonFLAVIN-ADENINE DINUCLEOTIDE
3IMD1Ligand/IonIMIDAZOLE

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
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 , 0T4 A:502 , HOH A:608 , HOH A:611BINDING SITE FOR RESIDUE FAD A 501
2AC2SOFTWAREGLY A:117 , GLY A:133 , LYS A:134 , TRP A:230 , GLN A:336 , VAL A:365 , ASN A:385 , ILE A:386 , CYS A:387 , FAD A:501 , HOH A:655BINDING SITE FOR RESIDUE 0T4 A 502
3AC3SOFTWARESER A:82 , ASP A:84 , SER B:82 , ASP B:84BINDING SITE FOR RESIDUE IMD A 503
4AC4SOFTWAREMET A:102 , ALA A:105 , LEU A:106 , LEU A:110 , TRP A:111 , VAL A:112BINDING SITE FOR RESIDUE IMD A 504
5AC5SOFTWARETRP B:16 , 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 , 0T4 B:502BINDING SITE FOR RESIDUE FAD B 501
6AC6SOFTWAREGLY B:117 , HIS B:132 , GLY B:133 , LYS B:134 , GLN B:336 , VAL B:365 , LYS B:367 , ASN B:385 , ILE B:386 , CYS B:387 , FAD B:501BINDING SITE FOR RESIDUE 0T4 B 502
7AC7SOFTWAREMET B:102 , LEU B:106 , LEU B:110 , TRP B:111 , VAL B:112 , MET B:191BINDING SITE FOR RESIDUE IMD B 503

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4FF6)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Pro A:237 -Pro A:238
2Pro B:237 -Pro B:238

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4FF6)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4FF6)

(-) Exons   (0, 0)

(no "Exon" information available for 4FF6)

(-) 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:423
                                                                                                                                                                                                                                                                                                                                                                                                                                                                       
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee........eeeeeee..hhhhhhhhhhhhhh....eeee...............eeee......eeeee....eeeee...hhhhhhhhhh...ee..........hhhhhhhh.....hhhhhhhhhh.eeeeeee.....eeee.....hhhhhhhhh.......eeeeeeee.ee....eeeeeeee..hhhhhhhhhhhhhhhhh.eeeeee...........eeeeeeee.hhhhh..................hhhhhhhhhhhhheeeeeeehhhhhh.eeeeeeeee..hhhhhhhhhhhhhhh.......eeeee.............eeeeeeeee...hhhhhhhhhhhhhhhh..ee........hhhhhhhhh.hhhhhhhhhhhhh......hhhhhhh... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ff6 A   7 TTTATRLTGWGRTAPSVANVLRTPDAEMIVKAVARVAESGRGAIARGLGRSYGDNAQNGGGLVIDMTPLNTIHSIDADTKLVDIDAGVNLDQLMKAALPFGLWVPVLPGTRQVTVGGAIACDIHGKNHHSAGSFGNHVRSMDLLTADGEIRHLTPTGEDAELFWATVGGNGLTGIIMRATIEMTPTSTAYFIADGDVTASLDETIALHSDGSEARYTYSSAWFDAISAPPKLGRAAVSRGRLATVEQLPAKLRSEPLKFDANKYTFGPIGELWYRKSGTYRGKVQNLTQFYHGFLQYQFVIPTEAVDEFKKIIGVIQASGHYSFLNVFKLFGPRNQAPLSFPIPGWNICVDFPIKDGLGKFVSELDRRVLEFGGRLYTAKDSRTTAETFHAMYPRVDEWISVRRKVDPLRVFASDMARRLELL 461
                                    16        26        36        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268|      293       303       313 ||    338       348       358       368       378       388       398       408       418       428       438       448       458   
                                                                 45|                                                                                                                                                                                                                         268|                            315|                                                                                                                                  
                                                                  48                                                                                                                                                                                                                          284                             331                                                                                                                                  


Chain B from PDB  Type:PROTEIN  Length:414
                                                                                                                                                                                                                                                                                                                                                                                                                                                              
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeeee........eeeeeee..hhhhhhhhhhhhhh....eeee...............eeee......eeeee....eeeee...hhhhhhhhhh...ee..........hhhhhhhh.....hhhhhhhhhh.eeeeeee.....eeee.....hhhhhhhhh.......eeeeeeee.ee.....eeeeeee..hhhhhhhhhh.hhhhhh.eeeeee...........eeeeeeee.hhhhh.............hhhhhhhhheeeeeehhhhhhh.eeeeeeeee..hhhhhhhhhhhhhhh.......eeeee.............eeeeeeeee...hhhhhhhhhhhhhhhh..ee........hhhhhhhhh.hhhhhhhhhhhhh......hhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4ff6 B   7 TTTATRLTGWGRTAPSVANVLRTPDAEMIVKAVARVAESGRGAIARGLGRSYGDNAQNGGGLVIDMTPLNTIHSIDADTKLVDIDAGVNLDQLMKAALPFGLWVPVLPGTRQVTVGGAIACDIHGKNHHSAGSFGNHVRSMDLLTADGEIRHLTPTGEDAELFWATVGGNGLTGIIMRATIEMTPTSTAYFIADGDVTASLDETIALHSDGSEARYTYSSAWFDAISAPPKLGRAAVSRGRLATVEQLPAKLRSEPLKFDGELWYRKSGTYRGKVQNLTQFYHGFLQYQFVIPTEAVDEFKKIIGVIQASGHYSFLNVFKLFGPRNQAPLSFPIPGWNICVDFPIKDGLGKFVSELDRRVLEFGGRLYTAKDSRTTAETFHAMYPRVDEWISVRRKVDPLRVFASDMARRLELL 461
                                    16        26        36        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268|      302       312  ||   337       347       357       367       377       387       397       407       417       427       437       447       457    
                                                                 45|                                                                                                                                                                                                                         268|                   315|                                                                                                                                  
                                                                  48                                                                                                                                                                                                                          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 4FF6)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4FF6)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4FF6)

(-) Gene Ontology  (14, 23)

Asymmetric Unit(hide GO term definitions)

 Visualization

(-) Interactive Views

Asymmetric Unit
  Complete Structure
    Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
    WebMol | AstexViewer[tm]@PDBe
(Java Applets, require no local installation except for Java; loading may be slow)
    STRAP
(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    RasMol
(require local installation)
    Molscript (VRML)
(requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)
 
  Ligands, Modified Residues, Ions
    0T4  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    FAD  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    IMD  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
    AC4  [ RasMol ]  +environment [ RasMol ]
    AC5  [ RasMol ]  +environment [ RasMol ]
    AC6  [ RasMol ]  +environment [ RasMol ]
    AC7  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Pro A:237 - Pro A:238   [ RasMol ]  
    Pro B:237 - Pro B:238   [ RasMol ]  
 
Biological Units
  Complete Structure
    Biological Unit 1  [ Jena3D ]
    Biological Unit 2  [ Jena3D ]

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym. Unit PNG format | Asym. Unit - sites PNG format | Biol. Unit 1 PNG format | Biol. Unit 1 - sites PNG format | Biol. Unit 2 PNG format ](automatic orientation, automatically generated)
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick
[ mono PDF format | stereo PDF format ](default orientation, automatically generated)

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  4ff6
    Family and Domain Information: ProDom | SYSTERS
    General Structural Information: GlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in Membranes: OPM
    Protein Surface: SURFACE
    Secondary Structure: DSSP (structure derived) | HSSP (homology derived)
    Structural Genomics: GeneCensus
    Structural Neighbours: CE | VAST
    Structure Classification: CATH | Dali | SCOP
    Validation and Original Data: BMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  DPRE1_MYCTO | P9WJF0
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
  DPRE1_MYCTU | P9WJF1
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  1.-.-.-
    General Enzyme Information: BRENDA | EC-PDB | Enzyme | IntEnz
    Pathway: KEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease Information: OMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related Information: GenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain Information: XDom
    Interatomic Contacts of Structural Units: CSU
    Ligand-protein Contacts: LPC
    Protein Cavities: castP
    Sequence and Secondary Structure: PDBCartoon
    Structure Alignment: STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence Browser: STING
 
Access by UniProt ID/Accession number
  DPRE1_MYCTO | P9WJF0
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)
  DPRE1_MYCTU | P9WJF1
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        DPRE1_MYCTO | P9WJF0: 4fdn 4fdo 4fdp 4feh 4ncr 4p8c 4p8h 4p8k 4p8l 4p8m 4p8n 4p8p 4p8t 4p8y
        DPRE1_MYCTU | P9WJF1: 4fdn 4fdo 4fdp 4feh 4kw5 4ncr 4p8c 4p8h 4p8k 4p8l 4p8m 4p8n 4p8p 4p8t 4p8y 4pfa 4pfd

(-) Related Entries Specified in the PDB File

4fdn 4fdo 4fdp 4feh