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
(-)Biological Unit 3
(-)Biological Unit 4
(-)Biological Unit 5
(-)Biological Unit 6
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)
Image Biological Unit 3
Biological Unit 3  (Jmol Viewer)
Image Biological Unit 4
Biological Unit 4  (Jmol Viewer)
Image Biological Unit 5
Biological Unit 5  (Jmol Viewer)
Image Biological Unit 6
Biological Unit 6  (Jmol Viewer)

(-) Description

Title :  STRUCTURES OF VACCINIA VIRUS URACIL-DNA GLYCOSYLASE IN NEW CRYSTAL FORMS
 
Authors :  N. Schormann, D. Chattopadhyay
Date :  09 Feb 12  (Deposition) - 20 Feb 13  (Release) - 29 Jun 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.80
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
Biol. Unit 3:  A  (1x)
Biol. Unit 4:  B  (1x)
Biol. Unit 5:  C  (1x)
Biol. Unit 6:  D  (1x)
Keywords :  Dna Binding Component, Viral Processivity Factor, Hydrolase, Glycosidase, Dna Repair (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  N. Schormann, C. I. Sommers, R. P. Ricciardi, D. Chattopadhyay
Analysis Of The Dimer Interface In Crystal Structures Of Vaccinia Virus Uracil Dna Glycosylase
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - URACIL-DNA GLYCOSYLASE
    Chains: A, B, C, D
    EC Number: 3.2.2.27
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET15B
    Expression System Strain: BL21(DE3)PLYSS ROSETTA
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: D4R, VACWR109
    Mutation: YES
    Organism Common: VACV
    Organism Scientific: VACCINIA VIRUS WESTERN RESERVE
    Organism Taxid: 696871
    Synonym: UDG

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): AB  
Biological Unit 2 (1x):   CD
Biological Unit 3 (1x): A   
Biological Unit 4 (1x):  B  
Biological Unit 5 (1x):   C 
Biological Unit 6 (1x):    D

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 4DOF)

(-) Sites  (0, 0)

(no "Site" information available for 4DOF)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (8, 8)

Asymmetric Unit
No.Residues
1Ala A:9 -Pro A:10
2Ser A:43 -Pro A:44
3Ala B:9 -Pro B:10
4Ser B:43 -Pro B:44
5Ala C:9 -Pro C:10
6Ser C:43 -Pro C:44
7Ala D:9 -Pro D:10
8Ser D:43 -Pro D:44

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 4)

Asymmetric Unit (1, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1U_DNA_GLYCOSYLASEPS00130 Uracil-DNA glycosylase signature.UNG_VACCA61-70
 
 
 		  4A:61-70
B:61-70
C:61-70
D:61-70
Biological Unit 1 (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1U_DNA_GLYCOSYLASEPS00130 Uracil-DNA glycosylase signature.UNG_VACCA61-70
 
 
 		  2A:61-70
B:61-70
-
-
Biological Unit 2 (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1U_DNA_GLYCOSYLASEPS00130 Uracil-DNA glycosylase signature.UNG_VACCA61-70
 
 
 		  2-
-
C:61-70
D:61-70
Biological Unit 3 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1U_DNA_GLYCOSYLASEPS00130 Uracil-DNA glycosylase signature.UNG_VACCA61-70
 
 
 		  1A:61-70
-
-
-
Biological Unit 4 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1U_DNA_GLYCOSYLASEPS00130 Uracil-DNA glycosylase signature.UNG_VACCA61-70
 
 
 		  1-
B:61-70
-
-
Biological Unit 5 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1U_DNA_GLYCOSYLASEPS00130 Uracil-DNA glycosylase signature.UNG_VACCA61-70
 
 
 		  1-
-
C:61-70
-
Biological Unit 6 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1U_DNA_GLYCOSYLASEPS00130 Uracil-DNA glycosylase signature.UNG_VACCA61-70
 
 
 		  1-
-
-
D:61-70

(-) Exons   (0, 0)

(no "Exon" information available for 4DOF)

(-) 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:218
 aligned with UNG_VACCA | Q91UM2 from UniProtKB/Swiss-Prot  Length:218

    Alignment length:218
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210        
            UNG_VACCA     1 MNSVTVSHAPYTITYHDDWEPVMSQLVEFYNEVASWLLRDETSPIPDKFFIQLKQPLRNKRVCVCGIDPYPKDGTGVPFESPNFTKKSIKEIASSISRLTGVIDYKGYNLNIIDGVIPWNYYLSCKLGETKSHAIYWDKISKLLLQHITKHVSVLYCLGKTDFSNIRAKLESPVTTIVGYHPAARDRQFEKDRSFEIINVLLELDNKAPINWAQGFIY 218
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeee......eeeehhhhhhhhhhhhhhhhhhhhhhh...ee.hhhhhhhhhhh......eeeee...................hhhhhhhhhhhhhhhh.....ee.hhhh..eeeee....ee......hhhhhhhhhhhhhhhhhh...eeeee................eeeee....hhhhhhhhhhhhhhhhhhhhhh.....hhhh.ee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------U_DNA_GLYC---------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4dof A   1 MNSVTVSHAPYTITYHNDWEPVMSQLVEFYNEVASWLLRDETSPIPDKFFIQLKQPLRNKRVCVCGIDPYPKDGTGVPFESPNFTKKSIKEIASSISRLTGVIDYKGYNLNIIDGVIPWNYYLSCKLGETKSHAIYWDKISKLLLQHITKHVSVLYCLGKTDFSNIRAKLESPVTTIVGYHPAARDRQFEKDRSFEIINVLLELDNKAPINWAQGFIY 218
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210        


Chain B from PDB  Type:PROTEIN  Length:218
 aligned with UNG_VACCA | Q91UM2 from UniProtKB/Swiss-Prot  Length:218

    Alignment length:218
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210        
            UNG_VACCA     1 MNSVTVSHAPYTITYHDDWEPVMSQLVEFYNEVASWLLRDETSPIPDKFFIQLKQPLRNKRVCVCGIDPYPKDGTGVPFESPNFTKKSIKEIASSISRLTGVIDYKGYNLNIIDGVIPWNYYLSCKLGETKSHAIYWDKISKLLLQHITKHVSVLYCLGKTDFSNIRAKLESPVTTIVGYHPAARDRQFEKDRSFEIINVLLELDNKAPINWAQGFIY 218
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eee......eee.hhhhhhhhhhhhhhhhhhhhhhhh..ee.hhhhhhhhhhh......eeeee...................hhhhhhhhhhhhhhhh.....ee.hhhh..eeeee....ee......hhhhhhhhhhhhhhhhh....eeeee....hhhhhhh.....eeeee.......hhhhhhhhhhhhhhhhhhh.....hhhh.ee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------U_DNA_GLYC---------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4dof B   1 MNSVTVSHAPYTITYHNDWEPVMSQLVEFYNEVASWLLRDETSPIPDKFFIQLKQPLRNKRVCVCGIDPYPKDGTGVPFESPNFTKKSIKEIASSISRLTGVIDYKGYNLNIIDGVIPWNYYLSCKLGETKSHAIYWDKISKLLLQHITKHVSVLYCLGKTDFSNIRAKLESPVTTIVGYHPAARDRQFEKDRSFEIINVLLELDNKAPINWAQGFIY 218
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210        


Chain C from PDB  Type:PROTEIN  Length:218
 aligned with UNG_VACCA | Q91UM2 from UniProtKB/Swiss-Prot  Length:218

    Alignment length:218
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210        
            UNG_VACCA     1 MNSVTVSHAPYTITYHDDWEPVMSQLVEFYNEVASWLLRDETSPIPDKFFIQLKQPLRNKRVCVCGIDPYPKDGTGVPFESPNFTKKSIKEIASSISRLTGVIDYKGYNLNIIDGVIPWNYYLSCKLGETKSHAIYWDKISKLLLQHITKHVSVLYCLGKTDFSNIRAKLESPVTTIVGYHPAARDRQFEKDRSFEIINVLLELDNKAPINWAQGFIY 218
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eee......eee.hhhhhhhhhhhhhhhhhhhhhhh...ee.hhhhhhhhhhh......eeeee...................hhhhhhhhhhhhhhhh.....ee.hhhh..eeeee....ee......hhhhhhhhhhhhhhhhh....eeeee................eeeee.......hhhhhhhhhhhhhhhhhh......hhhh.ee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------U_DNA_GLYC---------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4dof C   1 MNSVTVSHAPYTITYHNDWEPVMSQLVEFYNEVASWLLRDETSPIPDKFFIQLKQPLRNKRVCVCGIDPYPKDGTGVPFESPNFTKKSIKEIASSISRLTGVIDYKGYNLNIIDGVIPWNYYLSCKLGETKSHAIYWDKISKLLLQHITKHVSVLYCLGKTDFSNIRAKLESPVTTIVGYHPAARDRQFEKDRSFEIINVLLELDNKAPINWAQGFIY 218
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210        


Chain D from PDB  Type:PROTEIN  Length:218
 aligned with UNG_VACCA | Q91UM2 from UniProtKB/Swiss-Prot  Length:218

    Alignment length:218
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210        
            UNG_VACCA     1 MNSVTVSHAPYTITYHDDWEPVMSQLVEFYNEVASWLLRDETSPIPDKFFIQLKQPLRNKRVCVCGIDPYPKDGTGVPFESPNFTKKSIKEIASSISRLTGVIDYKGYNLNIIDGVIPWNYYLSCKLGETKSHAIYWDKISKLLLQHITKHVSVLYCLGKTDFSNIRAKLESPVTTIVGYHPAARDRQFEKDRSFEIINVLLELDNKAPINWAQGFIY 218
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeee......eeeehhhhhhhhhhhhhhhhhhhhhhh...ee.hhhhhhhhhhh......eeeee...................hhhhhhhhhhhhhhhh.....ee.hhhh..eeeee....ee......hhhhhhhhhhhhhhhhh....eeeee................eeeee.......hhhhhhhhhhhhhhhh........hhhh.ee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------U_DNA_GLYC---------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4dof D   1 MNSVTVSHAPYTITYHNDWEPVMSQLVEFYNEVASWLLRDETSPIPDKFFIQLKQPLRNKRVCVCGIDPYPKDGTGVPFESPNFTKKSIKEIASSISRLTGVIDYKGYNLNIIDGVIPWNYYLSCKLGETKSHAIYWDKISKLLLQHITKHVSVLYCLGKTDFSNIRAKLESPVTTIVGYHPAARDRQFEKDRSFEIINVLLELDNKAPINWAQGFIY 218
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210
   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 4DOF)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (7, 7)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D   (UNG_VACCA | Q91UM2)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0016787    hydrolase activity    Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
    GO:0016798    hydrolase activity, acting on glycosyl bonds    Catalysis of the hydrolysis of any glycosyl bond.
    GO:0016799    hydrolase activity, hydrolyzing N-glycosyl compounds    Catalysis of the hydrolysis of any N-glycosyl bond.
biological process
    GO:0006281    DNA repair    The process of restoring DNA after damage. Genomes are subject to damage by chemical and physical agents in the environment (e.g. UV and ionizing radiations, chemical mutagens, fungal and bacterial toxins, etc.) and by free radicals or alkylating agents endogenously generated in metabolism. DNA is also damaged because of errors during its replication. A variety of different DNA repair pathways have been reported that include direct reversal, base excision repair, nucleotide excision repair, photoreactivation, bypass, double-strand break repair pathway, and mismatch repair pathway.
    GO:0006974    cellular response to DNA damage stimulus    Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus indicating damage to its DNA from environmental insults or errors during metabolism.
    GO:0008152    metabolic process    The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation.

 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 4dof)
 
  Sites
(no "Sites" information available for 4dof)
 
  Cis Peptide Bonds
    Ala A:9 - Pro A:10   [ RasMol ]  
    Ala B:9 - Pro B:10   [ RasMol ]  
    Ala C:9 - Pro C:10   [ RasMol ]  
    Ala D:9 - Pro D:10   [ RasMol ]  
    Ser A:43 - Pro A:44   [ RasMol ]  
    Ser B:43 - Pro B:44   [ RasMol ]  
    Ser C:43 - Pro C:44   [ RasMol ]  
    Ser D:43 - Pro D:44   [ RasMol ]  
 
Biological Units
  Complete Structure
    Biological Unit 1  [ Jena3D ]
    Biological Unit 2  [ Jena3D ]
    Biological Unit 3  [ Jena3D ]
    Biological Unit 4  [ Jena3D ]
    Biological Unit 5  [ Jena3D ]
    Biological Unit 6  [ 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 | Biol. Unit 3 PNG format | Biol. Unit 4 PNG format | Biol. Unit 5 PNG format | Biol. Unit 6 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
  4dof
    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_VACCA | Q91UM2
    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_VACCA | Q91UM2
    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_VACCA | Q91UM2: 2owq 3nt7 4dog 4irb 4lzb 4qc9 4qca 5jx3

(-) Related Entries Specified in the PDB File

2owq THE STRUCTURE OF WTD4 WITH N-TERMINAL HIS-TAG IN TRIGONAL SPACE GROUP
4dog