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

(-) Description

Title :  STRUCTURE OF HYDROXYETHYLTHIAZOLE KINASE THIM FROM STAPHYLOCOCCUS AUREUS
 
Authors :  J. Drebes, M. Kuenz, R. J. Eberle, D. Oberthuer, H. Cang, C. Wrenger, C. B
Date :  16 Jul 15  (Deposition) - 23 Mar 16  (Release) - 23 Mar 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.09
Chains :  Asym. Unit :  A,B,C,D,E,F
Biol. Unit 1:  A,B,C  (1x)
Biol. Unit 2:  D,E,F  (1x)
Keywords :  Bacterial Thiamine Biosynthesis, Hydroxyethylthiazole Kinase, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. Drebes, M. Kunz, B. Windshugel, A. G. Kikhney, I. B. Muller, R. J. Eberle, D. Oberthur, H. Cang, D. I. Svergun, M. Perbandt, C. Betzel, C. Wrenger
Structure Of Thim From Vitamin B1 Biosynthetic Pathway Of Staphylococcus Aureus - Insights Into A Novel Pro-Drug Approach Addressing Mrsa Infections.
Sci Rep V. 6 22871 2016
PubMed-ID: 26960569  |  Reference-DOI: 10.1038/SREP22871

(-) Compounds

Molecule 1 - HYDROXYETHYLTHIAZOLE KINASE
    Chains: A, B, C, D, E, F
    EC Number: 2.7.1.50
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PASK-IBA3
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: THIM, SAR2181
    Organism Scientific: STAPHYLOCOCCUS AUREUS SUBSP. AUREUS MRSA252
    Organism Taxid: 282458
    Synonym: 4-METHYL-5-BETA-HYDROXYETHYLTHIAZOLE KINASE,THZ KINASE

 Structural Features

(-) Chains, Units

  123456
Asymmetric Unit : ABCDEF
Biological Unit 1 (1x): ABC   
Biological Unit 2 (1x):    DEF

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 5CM5)

(-) Sites  (0, 0)

(no "Site" information available for 5CM5)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5CM5)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 5CM5)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5CM5)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5CM5)

(-) Exons   (0, 0)

(no "Exon" information available for 5CM5)

(-) 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:262
                                                                                                                                                                                                                                                                                                      
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhh.eeeee....hhhhhhhhhhhh..eee...hhhhhhhhhhh..eeeee....hhhhhhhhhhhhhhhhhhh..eeee..hhhhhhhhhhhhhhhhhhh...eeeeehhhhhhhhh..............hhhhhhhhhhhhhh.eeeee...eeeee..eeeee...hhhhhhh.hhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhh.eee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5cm5 A   1 MNYLNNIRIENPLTICYTNDVVKNFTANGLLSIGASPAMSEAPEEAEEFYKVAQALLINIGTLTAQNEQDIIAIAQTANEAGLPIVFDPVAVGASTYRKQFCKLLLKSAKVSVIKGNASEILALIDDTATMKGTDSDANLDAVTIAKKAYAIYKTAIVITGKEDVIVQGDKAIVLANGSPLLARVTGAGCLLGGIIAGFLFRETEPDIEALIEAVSVFNIAAEVAAENENCGGPGTFSPLLLDTLYHLNETTYQQRIRIQEV 262
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260  


Chain B from PDB  Type:PROTEIN  Length:254
                                                                                                                                                                                                                                                                                              
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhh.eeeee....hhhhhhhhhhhh..eee...hhhhhhhhhhhh.eeeee....hhhhhhhhhhhhhhhhhhh..eeee..hhhhhhhhhhhhhhhhhhh...eeeeehhhhhhhhh.hhhhhhhhhhhhhh.eeeee...eeeee..eeeee...hhhhhhh..hhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhh.eeee..... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5cm5 B   1 MNYLNNIRIENPLTICYTNDVVKNFTANGLLSIGASPAMSEAPEEAEEFYKVAQALLINIGTLTAQNEQDIIAIAQTANEAGLPIVFDPVAVGASTYRKQFCKLLLKSAKVSVIKGNASEILALIDLDAVTIAKKAYAIYKTAIVITGKEDVIVQGDKAIVLANGSPLLARVTGAGCLLGGIIAGFLFRETEPDIEALIEAVSVFNIAAEVAAENENCGGPGTFSPLLLDTLYHLNETTYQQRIRIQEVEENLY 267
                                    10        20        30        40        50        60        70        80        90       100       110       120     ||143       153       163       173       183       193       203       213       223       233       243       253       263    
                                                                                                                                                       126|                                                                                                                               
                                                                                                                                                        140                                                                                                                               


Chain C from PDB  Type:PROTEIN  Length:258
                                                                                                                                                                                                                                                                                                  
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .hhhhhhhhhh.eeeee....hhhhhhhhhhhh..eee...hhhhhhhhhhhh.eeeee....hhhhhhhhhhhhhhhhhhh..eeee..hhhhhhhhhhhhhhhhhhh...eeeeehhhhhhhhhh.........hhhhhhhhhhhhhh.eeeee...eeeee..eeeee...hhhhhhh.hhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhh.eee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5cm5 C   1 MNYLNNIRIENPLTICYTNDVVKNFTANGLLSIGASPAMSEAPEEAEEFYKVAQALLINIGTLTAQNEQDIIAIAQTANEAGLPIVFDPVAVGASTYRKQFCKLLLKSAKVSVIKGNASEILALIDDTATMKGTNLDAVTIAKKAYAIYKTAIVITGKEDVIVQGDKAIVLANGSPLLARVTGAGCLLGGIIAGFLFRETEPDIEALIEAVSVFNIAAEVAAENENCGGPGTFSPLLLDTLYHLNETTYQQRIRIQEV 262
                                    10        20        30        40        50        60        70        80        90       100       110       120       130   ||  144       154       164       174       184       194       204       214       224       234       244       254        
                                                                                                                                                               134|                                                                                                                           
                                                                                                                                                                139                                                                                                                           


Chain D from PDB  Type:PROTEIN  Length:254
                                                                                                                                                                                                                                                                                              
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhh.eeeee....hhhhhhhhhhhh..eee...hhhhhhhhhhhh.eeeee....hhhhhhhhhhhhhhhhhhh..eeee..hhhhhhhhhhhhhhhhhhh...eeeeehhhhhhhhh....hhhhhhhhhhhhhh.eeeee...eeeee..eeeee...hhhhhhh.hhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhh.eeeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5cm5 D   1 MNYLNNIRIENPLTICYTNDVVKNFTANGLLSIGASPAMSEAPEEAEEFYKVAQALLINIGTLTAQNEQDIIAIAQTANEAGLPIVFDPVAVGASTYRKQFCKLLLKSAKVSVIKGNASEILALIDDANLDAVTIAKKAYAIYKTAIVITGKEDVIVQGDKAIVLANGSPLLARVTGAGCLLGGIIAGFLFRETEPDIEALIEAVSVFNIAAEVAAENENCGGPGTFSPLLLDTLYHLNETTYQQRIRIQEVEE 264
                                    10        20        30        40        50        60        70        80        90       100       110       120     ||140       150       160       170       180       190       200       210       220       230       240       250       260    
                                                                                                                                                       126|                                                                                                                               
                                                                                                                                                        137                                                                                                                               


Chain E from PDB  Type:PROTEIN  Length:249
                                                                                                                                                                                                                                                                                         
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhh.eeeee....hhhhhhhhhhhh..eee...hhhhhhhhhhhh.eeeee....hhhhhhhhhhhhhhhhhhh..eeee..hhhhhhhhhhhhhhhhhhh...eeeeehhhhhhhhh.hhhhhhhhhhhhhh.eeeee...eeeee..eeeee...hhhhhhh..hhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhh.eee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5cm5 E   1 MNYLNNIRIENPLTICYTNDVVKNFTANGLLSIGASPAMSEAPEEAEEFYKVAQALLINIGTLTAQNEQDIIAIAQTANEAGLPIVFDPVAVGASTYRKQFCKLLLKSAKVSVIKGNASEILALIDLDAVTIAKKAYAIYKTAIVITGKEDVIVQGDKAIVLANGSPLLARVTGAGCLLGGIIAGFLFRETEPDIEALIEAVSVFNIAAEVAAENENCGGPGTFSPLLLDTLYHLNETTYQQRIRIQEV 262
                                    10        20        30        40        50        60        70        80        90       100       110       120     ||143       153       163       173       183       193       203       213       223       233       243       253         
                                                                                                                                                       126|                                                                                                                          
                                                                                                                                                        140                                                                                                                          


Chain F from PDB  Type:PROTEIN  Length:248
                                                                                                                                                                                                                                                                                        
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhh.eeeee....hhhhhhhhhhhh..eee...hhhhhhhhhhhh.eeeee....hhhhhhhhhhhhhhhhhhh..eeee..hhhhhhhhhhhhhhhhhhh...eeeeehhhhhhhhh.hhhhhhhhhhhhhh.eeeee...eeeee..eeeee...hhhhhhh..hhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhh.ee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5cm5 F   1 MNYLNNIRIENPLTICYTNDVVKNFTANGLLSIGASPAMSEAPEEAEEFYKVAQALLINIGTLTAQNEQDIIAIAQTANEAGLPIVFDPVAVGASTYRKQFCKLLLKSAKVSVIKGNASEILALIDLDAVTIAKKAYAIYKTAIVITGKEDVIVQGDKAIVLANGSPLLARVTGAGCLLGGIIAGFLFRETEPDIEALIEAVSVFNIAAEVAAENENCGGPGTFSPLLLDTLYHLNETTYQQRIRIQE 261
                                    10        20        30        40        50        60        70        80        90       100       110       120     ||143       153       163       173       183       193       203       213       223       233       243       253        
                                                                                                                                                       126|                                                                                                                         
                                                                                                                                                        140
   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 5CM5)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5CM5)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5CM5)

(-) Gene Ontology  (10, 10)

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
(no "Ligands, Modified Residues, Ions" information available for 5cm5)
 
  Sites
(no "Sites" information available for 5cm5)
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 5cm5)
 
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 | Biol. Unit 1 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
  5cm5
    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
  THIM_STAAR | Q6GEY3
    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)
  2.7.1.50
    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
  THIM_STAAR | Q6GEY3
    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
        THIM_STAAR | Q6GEY3: 5cga 5cge 5coj

(-) Related Entries Specified in the PDB File

5cga THE SAME PROTEIN WITH SUBSTRATE ANALOGS.
5cge THE SAME PROTEIN WITH SUBSTRATE ANALOGS.