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

(-) Description

Title :  CRYSTAL STRUCTURE OF MYCOBACTERIUM TUBERCULOSIS URACIL-DNA GLYCOSYLASE IN COMPLEX WITH URACIL, FORM III
 
Authors :  S. M. Arif, K. Geethanandan, P. Mishra, A. Surolia, U. Varshney, M. Vija
Date :  25 Oct 14  (Deposition) - 15 Jul 15  (Release) - 22 Jul 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.44
Chains :  Asym./Biol. Unit :  A
Keywords :  Dna-Repair, Excision Repair, Conformational Selection, Ligand- Binding, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. M. Arif, K. Geethanandan, P. Mishra, A. Surolia, U. Varshney, M. Vijayan
Structural Plasticity In Mycobacterium Tuberculosis Uracil-Dna Glycosylase (Mtung) And Its Functional Implications.
Acta Crystallogr. , Sect. D V. 71 1514 2015
PubMed-ID: 26143923  |  Reference-DOI: 10.1107/S1399004715009311
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - URACIL-DNA GLYCOSYLASE
    Chains: A
    EC Number: 3.2.2.27
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PRSETB MTUUDG
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: UNG, RV2976C, MTCY349.11
    Organism Scientific: MYCOBACTERIUM TUBERCULOSIS
    Organism Taxid: 83332
    Strain: ATCC 25618 / H37RV
    Synonym: UDG

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (2, 3)
No.NameCountTypeFull Name
1CL2Ligand/IonCHLORIDE ION
2URA1Ligand/IonURACIL

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY A:66 , GLN A:67 , ASP A:68 , TYR A:70 , SER A:80 , PHE A:81 , ASN A:127 , HOH A:521 , HOH A:586 , HOH A:608binding site for residue URA A 301
2AC2SOFTWAREARG A:41 , ARG A:133 , HOH A:415 , HOH A:618binding site for residue CL A 302
3AC3SOFTWARESER A:93 , HOH A:515 , HOH A:630binding site for residue CL A 303

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (3, 4)

Asymmetric/Biological Unit
No.Residues
1Leu A:43 -Pro A:44
2Arg A:88 -Pro A:89
3Ser A:189 -Pro A:190

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4WRV)

(-) Sequences/Alignments

Asymmetric/Biological 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:223
                                                                                                                                                                                                                                                               
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhh.eeeee........................hhhhhhhhhhhhhhhh........hhhhhhh.eeeee................hhhhhhhhhhhhhhhh...eeeee...hhhhhhhhhh....eee.....hhhhh.......hhhhhhhhhhhhh.......... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4wrv A   5 PLSELVERGWAAALEPVADQVAHMGQFLRAEIAAGRRYLPAGSNVLRAFTFPFDNVRVLIVGQDPYPTPGHAVGLSFSVAPDVRPWPRSLANIFDEYTADLGYPLPSNGDLTPWAQRGVLLLNRVLTVRPSNPASHRGKGWEAVTECAIRALAARAAPLVAILWGRDASTLKPMLAAGNCVAIESPHPSPLSASRGFFGSRPFSRANELLVGMGAEPIDWRLP 227
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224
   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 4WRV)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (9, 9)

Asymmetric/Biological Unit(hide GO term definitions)

 Visualization

(-) Interactive Views

Asymmetric/Biological 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
    CL  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    URA  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Arg A:88 - Pro A:89   [ RasMol ]  
    Leu A:43 - Pro A:44   [ RasMol ]  
    Ser A:189 - Pro A:190   [ RasMol ]  
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym./Biol. Unit PNG format | Asym./Biol. Unit - 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
  4wrv
    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
  UNG_MYCTU | P9WFQ9
    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)
  3.2.2.27
    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
  UNG_MYCTU | P9WFQ9
    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
        UNG_MYCTU | P9WFQ9: 2zhx 3a7n 4wpk 4wpl 4wru 4wrw 4wrx 4wry 4wrz 4ws0 4ws1 4ws2 4ws3 4ws4 4ws5 4ws6 4ws7 4ws8

(-) Related Entries Specified in the PDB File

4wru 4wrw 4wrx 4wry 4wrz 4ws0 4ws1 4ws2 4ws3 4ws4 4ws5 4ws6 4ws7 4ws8