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
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)

(-) Description

Title :  STRUCTURE OF MYCOBACTERIUM TUBERCULOSIS TRANSCRIPTIONAL REGULATORY REPRESSOR PROTEIN (ETHR) IN COMPLEX WITH FRAGMENT 7G9.
 
Authors :  V. Mendes, D. S. -H. Chan, S. E. Thomas, B. Mcconnell, D. Matak-Vinkovic A. G. Coyne, C. Abell, T. L. Blundell
Date :  23 Jan 17  (Deposition) - 31 May 17  (Release) - 21 Jun 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.93
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Ethr, Repressor, Tetr, Mycobacterium Tuberculosis, Transcription (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  D. S. Chan, V. Mendes, S. E. Thomas, B. N. Mcconnell, D. Matak-Vinkovic A. G. Coyne, T. L. Blundell, C. Abell
Fragment Screening Against The Ethr-Dna Interaction By Native Mass Spectrometry.
Angew. Chem. Int. Ed. Engl. V. 56 7488 2017
PubMed-ID: 28513917  |  Reference-DOI: 10.1002/ANIE.201702888

(-) Compounds

Molecule 1 - HTH-TYPE TRANSCRIPTIONAL REGULATOR ETHR
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Taxid: 469008
    Gene: ETHR, ETAR, RV3855
    Organism Scientific: MYCOBACTERIUM TUBERCULOSIS H37RV
    Organism Taxid: 83332

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (2x): A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 3)

Asymmetric Unit (2, 3)
No.NameCountTypeFull Name
1EDO2Ligand/Ion1,2-ETHANEDIOL
2ZHA1Ligand/Ion~{N}-(5-OXIDANYLIDENE-7,8-DIHYDRO-6~{H}-NAPHTHALEN-2-YL)ETHANAMIDE
Biological Unit 1 (2, 6)
No.NameCountTypeFull Name
1EDO4Ligand/Ion1,2-ETHANEDIOL
2ZHA2Ligand/Ion~{N}-(5-OXIDANYLIDENE-7,8-DIHYDRO-6~{H}-NAPHTHALEN-2-YL)ETHANAMIDE

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETRP A:103 , GLY A:106 , ILE A:107 , PHE A:110 , TYR A:148 , THR A:149 , ASN A:176 , ASN A:179 , TRP A:207binding site for residue ZHA A 301
2AC2SOFTWAREPHE A:111 , GLU A:112 , GLY A:115 , GLU A:196binding site for residue EDO A 302
3AC3SOFTWAREASP A:98 , ARG A:99binding site for residue EDO A 303

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5MXK)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Gln A:191 -Pro A:192

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5MXK)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5MXK)

(-) Exons   (0, 0)

(no "Exon" information available for 5MXK)

(-) 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:193
                                                                                                                                                                                                                                 
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhh.hhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5mxk A  22 GDDRELAILATAENLLEDRPLADISVDDLAKGAGISRPTFYFYFPSKEAVLLTLLDRVVNQADMALQTLAENPADTDRENMWRTGINVFFETFGSHKAVTRAGQAARATSVEVAELWSTFMQKWIAYTAAVIDAERDRGAAPRTLPAHELATALNLMNERTLFASFAGEQPSVPEARVLDTLVHIWVTSIYGE 214
                                    31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211
   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 5MXK)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5MXK)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5MXK)

(-) Gene Ontology  (7, 7)

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
    EDO  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    ZHA  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Gln A:191 - Pro A:192   [ RasMol ]  
 
Biological Unit
  Complete Structure
    Biological Unit 1  [ 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 ](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
  5mxk
    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
  ETHR_MYCTU | P9WMC1
    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)
  (no 'Enzyme Classificator' available)
    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
  ETHR_MYCTU | P9WMC1
    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
        ETHR_MYCTU | P9WMC1: 1t56 1u9n 1u9o 3g1l 3g1m 3g1o 3o8g 3o8h 3q0u 3q0v 3q0w 3q3s 3qpl 3sdg 3sfi 3tp0 3tp3 4dw6 4m3b 4m3d 4m3e 4m3f 4m3g 5eyr 5ezg 5ezh 5f04 5f08 5f0c 5f0f 5f0h 5f1j 5f27 5j1r 5j1u 5j1y 5j3l 5mwo

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 5MXK)