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(-) Description

Title :  VACCINIA VIRUS D4 R167A MUTANT /A20(1-50)
 
Authors :  C. Contesto-Richefeu, N. Tarbouriech, X. Brazzolotto, W. P. Burmeist C. N. Peyrefitte, F. Iseni
Date :  26 Apr 16  (Deposition) - 14 Sep 16  (Release) - 28 Sep 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.79
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  B,D  (1x)
Biol. Unit 2:  A,C  (1x)
Keywords :  Dna Polymerase Processivity Factor, Dna Binding, Dna Polymerase Binding, Hydrolase-Replication Complex, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  C. Contesto-Richefeu, N. Tarbouriech, X. Brazzolotto, W. P. Burmeister, C. N. Peyrefitte, F. Iseni
Structural Analysis Of Point Mutations At The Vaccinia Viru A20/D4 Interface.
Acta Crystallogr. , Sect. F V. 72 687 2016
PubMed-ID: 27599859  |  Reference-DOI: 10.1107/S2053230X16011778

(-) Compounds

Molecule 1 - URACIL-DNA GLYCOSYLASE
    Chains: B, A
    EC Number: 3.2.2.27
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Taxid: 469008
    Gene: UNG, D4R
    Mutation: YES
    Organism Common: VACV
    Organism Scientific: VACCINIA VIRUS (STRAIN COPENHAGEN)
    Organism Taxid: 10249
    Strain: COPENHAGEN
    Synonym: UDG
 
Molecule 2 - DNA POLYMERASE PROCESSIVITY FACTOR COMPONENT A20
    Chains: D, C
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Taxid: 469008
    Gene: A20R
    Organism Common: VACV
    Organism Scientific: VACCINIA VIRUS (STRAIN COPENHAGEN)
    Organism Taxid: 10249
    Other Details: FRAGMENT: N-TERMINAL RESIDUES 1-50
    Strain: COPENHAGEN

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x):  B D
Biological Unit 2 (1x): A C 

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 6)

Asymmetric Unit (1, 6)
No.NameCountTypeFull Name
1SO46Ligand/IonSULFATE ION
Biological Unit 1 (1, 4)
No.NameCountTypeFull Name
1SO44Ligand/IonSULFATE ION
Biological Unit 2 (1, 2)
No.NameCountTypeFull Name
1SO42Ligand/IonSULFATE ION

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY B:159 , LYS B:160 , THR B:161 , TYR B:180 , HIS B:181 , ALA B:184binding site for residue SO4 B 301
2AC2SOFTWARETYR B:70 , PRO B:71 , SER B:88 , HIS B:181 , SO4 B:304binding site for residue SO4 B 302
3AC3SOFTWARELYS B:86 , LYS B:87binding site for residue SO4 B 303
4AC4SOFTWAREGLY B:66 , ASP B:68 , PRO B:69 , TYR B:70 , PHE B:79 , ASN B:120 , SO4 B:302binding site for residue SO4 B 304
5AC5SOFTWAREGLY A:159 , LYS A:160 , THR A:161 , HIS A:181 , ALA A:184binding site for residue SO4 A 301
6AC6SOFTWARETHR A:85 , LYS A:86 , LYS A:87binding site for residue SO4 A 302

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (4, 4)

Asymmetric Unit
No.Residues
1Ala B:9 -Pro B:10
2Ser B:43 -Pro B:44
3Ala A:9 -Pro A:10
4Ser A:43 -Pro A:44

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5JKS)

(-) 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:220
                                                                                                                                                                                                                                                            
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee......eeeee..hhhhhhhhhhhhhhhhhhhhhh.ee......hhhhhh......eeeee...................hhhhhhhhhhhhhhhh.....ee.hhhh..eeeee....ee......hhhhhhhhhhhhhhhhh....eeeee.......hhhhh....eeeee....hhhhhhhhhhhhhhhhhhhhhh.....hhhh.ee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5jks A  -1 DPMNSVTVSHAPYTITYHDDWEPVMSQLVEFYNEVASWLLRDETSPIPDKFFIQLKQPLRNKRVCVCGIDPYPKDGTGVPFESPNFTKKSIKEIASSISRLTGVIDYKGYNLNIIDGVIPWNYYLSCKLGETKSHAIYWDKISKLLLQHITKHVSVLYCLGKTDFSNIAAKLESPVTTIVGYHPAARDRQFEKDRSFEIINVLLELDNKVPINWAQGFIY 218
                                     8        18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218


Chain B from PDB  Type:PROTEIN  Length:221
                                                                                                                                                                                                                                                             
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeee......eeeee..hhhhhhhhhhhhhhhhhhhhh..ee.hhhhhhhhhhh......eeeee...................hhhhhhhhhhhhhhhh.....ee.hhhh..eeeee....ee......hhhhhhhhhhhhhhhhhh...eeeee......hhhhhh....eeeee....hhhhhhhh.hhhhhhhhhhhh......hhhh.ee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5jks B  -2 QDPMNSVTVSHAPYTITYHDDWEPVMSQLVEFYNEVASWLLRDETSPIPDKFFIQLKQPLRNKRVCVCGIDPYPKDGTGVPFESPNFTKKSIKEIASSISRLTGVIDYKGYNLNIIDGVIPWNYYLSCKLGETKSHAIYWDKISKLLLQHITKHVSVLYCLGKTDFSNIAAKLESPVTTIVGYHPAARDRQFEKDRSFEIINVLLELDNKVPINWAQGFIY 218
                                     7        17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217 


Chain C from PDB  Type:PROTEIN  Length:51
                                                                                   
               SCOP domains --------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhh....... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------- Transcript
                 5jks C   0 AMTSSADLTNLKELLSLYKSLRFSDSAAIEKYNSLVEWGTSTYWKIGVQKV  50
                                     9        19        29        39        49 


Chain D from PDB  Type:PROTEIN  Length:51
                                                                                   
               SCOP domains --------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhh........ Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------- Transcript
                 5jks D   0 AMTSSADLTNLKELLSLYKSLRFSDSAAIEKYNSLVEWGTSTYWKIGVQKV  50
                                     9        19        29        39        49
   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 5JKS)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (10, 12)

Asymmetric Unit(hide GO term definitions)

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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        A20_VACCC | P20995: 4od8 4oda 4ygm 4yig 5jkr 5jkt
        UNG_VACCC | P20536: 4od8 4oda 4ygm 4yig 5jkr 5jkt

(-) Related Entries Specified in the PDB File

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