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(-) Description

Title :  THE CRYSTAL STRUCTURE OF ASFVPOLX:DNA1 BINARY COMPLEX
 
Authors :  Y. Q. Chen, J. Zhang, J. H. Gan
Date :  23 Jan 16  (Deposition) - 18 Jan 17  (Release) - 18 Jan 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.20
Chains :  Asym. Unit :  A,B,C,D,E,F,G,H
Biol. Unit 1:  A,C,D,E  (1x)
Biol. Unit 2:  B,F,G,H  (1x)
Keywords :  Asfv, Polx, Transferase-Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Y. Q. Chen, J. Zhang, J. H. Gan
The Crystal Structure Of Asfvpolx: 1Nt-Gap(P) Dna1: Dgtp Ternary Complex.
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - DNA POLYMERASE BETA-LIKE PROTEIN
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: O174L
    Organism Common: ASFV
    Organism Scientific: AFRICAN SWINE FEVER VIRUS
    Organism Taxid: 10497
    Synonym: PO174L, POLX
 
Molecule 2 - DNA (5'- D(*CP*GP*TP*TP*CP*TP*AP*TP*CP*TP*GP*TP*AP*CP*TP*CP*AP*C)-3'
    Chains: C, F
    Engineered: YES
    Organism Scientific: SYNTHETIC CONSTRUCT
    Organism Taxid: 32630
    Synthetic: YES
 
Molecule 3 - DNA (5'-D(*GP*TP*GP*AP*GP*TP*AP*CP*A)-3')
    Chains: D, G
    Engineered: YES
    Organism Scientific: SYNTHETIC CONSTRUCT
    Organism Taxid: 32630
    Synthetic: YES
 
Molecule 4 - DNA (5'-D(P*AP*TP*AP*GP*AP*AP*CP*G)-3')
    Chains: E, H
    Engineered: YES
    Organism Scientific: SYNTHETIC CONSTRUCT
    Organism Taxid: 32630
    Synthetic: YES

 Structural Features

(-) Chains, Units

  12345678
Asymmetric Unit : ABCDEFGH
Biological Unit 1 (1x): A CDE   
Biological Unit 2 (1x):  B   FGH

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 6)

Asymmetric Unit (2, 6)
No.NameCountTypeFull Name
1DGT2Ligand/Ion2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE
2MN4Ligand/IonMANGANESE (II) ION
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1DGT1Ligand/Ion2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE
2MN-1Ligand/IonMANGANESE (II) ION
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1DGT1Ligand/Ion2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE
2MN-1Ligand/IonMANGANESE (II) ION

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWARESER A:39 , ARG A:42 , ASN A:48 , ASP A:49 , ASP A:51 , HIS A:115 , PHE A:116 , THR A:117 , GLY A:118 , VAL A:120 , LEU A:123 , ARG A:127 , MN A:202 , MN A:203 , HOH A:301 , HOH A:303 , HOH A:306 , HOH A:309 , DC C:9 , DA D:9binding site for residue DGT A 201
2AC2SOFTWAREASP A:49 , ASP A:51 , DGT A:201 , MN A:203 , HOH A:301binding site for residue MN A 202
3AC3SOFTWAREASP A:49 , ASP A:51 , ASP A:100 , DGT A:201 , MN A:202binding site for residue MN A 203
4AC4SOFTWAREGLY B:38 , SER B:39 , ARG B:42 , ASN B:48 , ASP B:49 , ASP B:51 , HIS B:115 , PHE B:116 , THR B:117 , GLY B:118 , VAL B:120 , LEU B:123 , ARG B:127 , MN B:202 , MN B:203 , HOH B:302 , HOH B:304 , HOH B:307 , HOH B:326 , DC F:9 , DA G:9binding site for residue DGT B 201
5AC5SOFTWAREASP B:49 , ASP B:51 , DGT B:201 , MN B:203 , HOH B:304binding site for residue MN B 202
6AC6SOFTWAREASP B:49 , ASP B:51 , ASP B:100 , DGT B:201 , MN B:202binding site for residue MN B 203

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Gly A:118 -Pro A:119
2Gly B:118 -Pro B:119

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5HRI)

(-) 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:175
                                                                                                                                                                                                               
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eehhhhhhhhhhhh..eeeee..eeee.hhh.eeehhhhhh...ee..eeeeeee.hhhhhhh....eee....eeeeee...eeeeeeee..eeeeeeeeeee..hhhhhhhhhhhhhhhhhhhhhhhhhh..ee....eee..ee......hhhhhhhhh.....hhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5hri A   0 GMLTLIQGKKIVNHLRSRLAFEYNGQLIKILSKNIVAVGSLRREEKMLNDVDLLIIVPEKKLLKHVLPNIRIKGLSFSVKVCGERKCVLFIEWEKKTYQLDLFTALAEEKPYAIFHFTGPVSYLIRIRAALKKKNYKLNQYGLFKNQTLVPLKITTEKELIKELGFTYRIPKKRL 174
                                     9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169     


Chain B from PDB  Type:PROTEIN  Length:176
                                                                                                                                                                                                                
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eehhhhhhhhhhhh..eeeee..eeee.hhh.eeehhhhhh...ee..eeeeeee.hhhhh......eee....eeeeee...eeeeeeee..eeeeeeeeeee..hhhhhhhhhhhhhhhhhhhhhhhhhh..ee....eee..ee......hhhhhhhhh.....hhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5hri B  -1 GGMLTLIQGKKIVNHLRSRLAFEYNGQLIKILSKNIVAVGSLRREEKMLNDVDLLIIVPEKKLLKHVLPNIRIKGLSFSVKVCGERKCVLFIEWEKKTYQLDLFTALAEEKPYAIFHFTGPVSYLIRIRAALKKKNYKLNQYGLFKNQTLVPLKITTEKELIKELGFTYRIPKKRL 174
                                     8        18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168      


Chain C from PDB  Type:DNA  Length:18
                                                  
                 5hri C   1 CGTTCTATCTGTACTCAC  18
                                    10        


Chain D from PDB  Type:DNA  Length:9
                                         
                 5hri D   1 GTGAGTACA   9


Chain E from PDB  Type:DNA  Length:8
                                        
                 5hri E   1 ATAGAACG   8


Chain F from PDB  Type:DNA  Length:18
                                                  
                 5hri F   1 CGTTCTATCTGTACTCAC  18
                                    10        


Chain G from PDB  Type:DNA  Length:9
                                         
                 5hri G   1 GTGAGTACA   9


Chain H from PDB  Type:DNA  Length:8
                                        
                 5hri H   1 ATAGAACG   8
   Legend:   → Mismatch (orange background)
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    → 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 5HRI)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (0, 0)

Asymmetric Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 5HRI)

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 Related Entries

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UniProtKB/TrEMBL
        A0A0A1E3N6_A | A0A0A1E3N6: 5hr9 5hrb 5hrd 5hre 5hrf 5hrg 5hrh 5hrk 5hrl

(-) Related Entries Specified in the PDB File

5hr9 5hrb 5hrd 5hre 5hrf 5hrg 5hrh 5hrk 5hrl