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 :  CRYSTAL STRUCTURE OF VACCINIA VIRUS URACIL-DNA GLYCOSYLASE MUTANT 3GD4
 
Authors :  D. Sartmatova, T. Nash, N. Schormann, M. Nuth, R. Ricciardi, S. Banerje D. Chattopadhyay
Date :  09 May 14  (Deposition) - 13 May 15  (Release) - 29 Jun 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.26
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
Keywords :  Dna Repair Enzyme, Component Of Processivity Factor, A20, Dna, Poxvirus, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  D. Sartmatova, T. Nash, N. Schormann, M. Nuth, R. Ricciardi, S. Banerjee, D. Chattopadhyay
Crystal Structure Of Vaccinia Virus Uracil-Dna Glycosylase Mutant 3Gd4
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - URACIL-DNA GLYCOSYLASE
    Chains: A, C, D, B
    EC Number: 3.2.2.27
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET15B
    Expression System Strain: ROSETTA(DE3)PLYSS
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: ACAM3000_MVA_101, D4, MVA101R, UNG
    Mutation: YES
    Organism Common: VACV
    Organism Scientific: VACCINIA VIRUS
    Organism Taxid: 126794
    Strain: WESTERN RESERVE, D4R, VACWR109
    Synonym: UDG

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): AB  
Biological Unit 2 (1x):   CD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 13)

Asymmetric Unit (2, 13)
No.NameCountTypeFull Name
1EDO8Ligand/Ion1,2-ETHANEDIOL
2SO45Ligand/IonSULFATE ION
Biological Unit 1 (2, 9)
No.NameCountTypeFull Name
1EDO6Ligand/Ion1,2-ETHANEDIOL
2SO43Ligand/IonSULFATE ION
Biological Unit 2 (2, 4)
No.NameCountTypeFull Name
1EDO2Ligand/Ion1,2-ETHANEDIOL
2SO42Ligand/IonSULFATE ION

(-) Sites  (13, 13)

Asymmetric Unit (13, 13)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREGLY A:159 , LYS A:160 , THR A:161 , TYR A:180 , HIS A:181 , ALA A:184 , HOH A:456BINDING SITE FOR RESIDUE SO4 A 301
02AC2SOFTWAREPRO A:69 , TYR A:70 , PHE A:79 , ASN A:120 , HOH A:413BINDING SITE FOR RESIDUE EDO A 302
03AC3SOFTWAREGLN A:55 , ASN A:59 , LYS A:60BINDING SITE FOR RESIDUE EDO A 303
04AC4SOFTWARETYR A:11 , THR A:12 , GLU D:196 , ASN D:199BINDING SITE FOR RESIDUE EDO A 304
05AC5SOFTWAREGLU A:32 , SER A:35BINDING SITE FOR RESIDUE EDO A 305
06AC6SOFTWAREGLY C:159 , LYS C:160 , THR C:161 , TYR C:180 , HIS C:181 , ALA C:184 , HOH C:434BINDING SITE FOR RESIDUE SO4 C 301
07AC7SOFTWAREASP C:68 , PRO C:69 , TYR C:70 , PHE C:79 , ASN C:120 , HOH C:403BINDING SITE FOR RESIDUE EDO C 302
08AC8SOFTWAREGLY D:159 , LYS D:160 , THR D:161 , GLY D:179 , TYR D:180 , HIS D:181 , HOH D:438BINDING SITE FOR RESIDUE SO4 D 301
09AC9SOFTWAREPRO D:69 , TYR D:70 , PRO D:78 , PHE D:79 , ASN D:120 , HOH D:405 , HOH D:416 , HOH D:439BINDING SITE FOR RESIDUE EDO D 302
10BC1SOFTWAREILE A:103 , GLY B:159 , LYS B:160 , THR B:161 , TYR B:180 , HIS B:181 , HOH B:412BINDING SITE FOR RESIDUE SO4 B 301
11BC2SOFTWARESER B:81 , PRO B:82 , ASN B:83 , PHE B:84 , THR B:85 , LYS B:86BINDING SITE FOR RESIDUE SO4 B 302
12BC3SOFTWARELYS A:90 , LYS B:87 , ARG B:185 , HOH B:405BINDING SITE FOR RESIDUE EDO B 303
13BC4SOFTWAREARG B:185BINDING SITE FOR RESIDUE EDO B 304

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4QC9)

(-) Cis Peptide Bonds  (9, 9)

Asymmetric Unit
No.Residues
1Ala A:9 -Pro A:10
2Ser A:43 -Pro A:44
3Ala C:9 -Pro C:10
4Ser C:43 -Pro C:44
5Ala D:9 -Pro D:10
6Ser D:43 -Pro D:44
7Ala B:9 -Pro B:10
8Ser B:43 -Pro B:44
9Gly B:172 -Gly B:173

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4QC9)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4QC9)

(-) Exons   (0, 0)

(no "Exon" information available for 4QC9)

(-) 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:219
                                                                                                                                                                                                                                                           
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee......eeeee..hhhhhhhhhhhhhhhhhhhh...ee.hhhhhhhhhhh......eeeee...................hhhhhhhhhhhhhhhh.....ee.hhhh..eeeee....ee......hhhhhhhhhhhhhhhhh....eeeee.........ee.....eeeee.............hhhhhhhhhhhhh.....hhhh.ee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4qc9 A   0 HMNSVTVSHAPYTITYHNDWEPVMSQLVEFYNEVASWLLRDETSPIPDKFFIQLKQPLRNKRVCVCGIDPYPKDGTGVPFESPNFTKKSIKEIASSISRLTGVIDYKGYNLNIIDGVIPWNYYLSCKLGETKSHAIYWDKISKLLLQHITKHVSVLYCLGKTDFSNIRAKLGGGVTTIVGYHPAARDRQFEKDRSFEIINVLLELDNKAPINWAQGFIY 218
                                     9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209         


Chain B from PDB  Type:PROTEIN  Length: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........ee......eeeee........hhhhhhhhhhhhhhhhhh.....hhhh.ee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4qc9 B   1 MNSVTVSHAPYTITYHNDWEPVMSQLVEFYNEVASWLLRDETSPIPDKFFIQLKQPLRNKRVCVCGIDPYPKDGTGVPFESPNFTKKSIKEIASSISRLTGVIDYKGYNLNIIDGVIPWNYYLSCKLGETKSHAIYWDKISKLLLQHITKHVSVLYCLGKTDFSNIRAKLGGGVTTIVGYHPAARDRQFEKDRSFEIINVLLELDNKAPINWAQGFIY 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
                                                                                                                                                                                                                                                          
               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.........ee....eeeee.............hhhhhhhhhhhhh.....hhhh.ee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4qc9 C   0 HMNSVTVSHAPYTITYHNDWEPVMSQLVEFYNEVASWLLRDETSPIPDKFFIQLKQPLRNKRVCVCGIDPYPKDGTGVPFESPNFTKKSIKEIASSISRLTGVIDYKGYNLNIIDGVIPWNYYLSCKLGETKSHAIYWDKISKLLLQHITKHVSVLYCLGKTDFSNIRAKLGGVTTIVGYHPAARDRQFEKDRSFEIINVLLELDNKAPINWAQGFIY 218
                                     9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169||     180       190       200       210        
                                                                                                                                                                                                    170|                                              
                                                                                                                                                                                                     172                                              


Chain D from PDB  Type:PROTEIN  Length:220
                                                                                                                                                                                                                                                            
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee......eeeee..hhhhhhhhhhhhhhhhhhhh...ee.hhhhhhhhhhh......eeeee...................hhhhhhhhhhhhhhhh.....ee.hhhh..eeeee....ee......hhhhhhhhhhhhhhhhh....eeeee........ee......eeeee.............hhhhhhhhhhhhh.....hhhh.ee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4qc9 D  -1 SHMNSVTVSHAPYTITYHNDWEPVMSQLVEFYNEVASWLLRDETSPIPDKFFIQLKQPLRNKRVCVCGIDPYPKDGTGVPFESPNFTKKSIKEIASSISRLTGVIDYKGYNLNIIDGVIPWNYYLSCKLGETKSHAIYWDKISKLLLQHITKHVSVLYCLGKTDFSNIRAKLGGGVTTIVGYHPAARDRQFEKDRSFEIINVLLELDNKAPINWAQGFIY 218
                                     8        18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218
   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 4QC9)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4QC9)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4QC9)

(-) 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 ]
    SO4  [ 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 ]
    AC8  [ RasMol ]  +environment [ RasMol ]
    AC9  [ RasMol ]  +environment [ RasMol ]
    BC1  [ RasMol ]  +environment [ RasMol ]
    BC2  [ RasMol ]  +environment [ RasMol ]
    BC3  [ RasMol ]  +environment [ RasMol ]
    BC4  [ RasMol ]  +environment [ RasMol ]
 
  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 ]  
    Gly B:172 - Gly B:173   [ 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 ]

(-) 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
  4qc9
    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 4dof 4dog 4irb 4lzb 4qca 5jx3

(-) Related Entries Specified in the PDB File

4dof HIS-TAGGED WILD TYPE VACCINIA VIRUS URACIL-DNA GLYCOSYLASE
4dog TAG-FREE WILD TYPE VACCINIA VIRUS URACIL-DNA GLYCOSYLASE
4irb DELETION MUTANT OF D4
4lzb VACCINIA VIRUS URACIL-DNA GLYCOSYLASE-URACIL COMPLEX
4qca
4qcb