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(-) Description

Title :  THE CRYSTAL STRUCTURE OF ASFVPOLX(H115F MUTANT): 1NT-GAP(P) DNA2:DGTP TERNARY 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 :  2.90
Chains :  Asym. Unit :  A,B,C,D,E,F,G,H
Biol. Unit 1:  A,F,G,H  (1x)
Biol. Unit 2:  B,C,D,E  (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 Se-Asfvpolx(L52/163M Mutant) In Complex With 1Nt-Gap Dna1
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - DNA POLYMERASE BETA-LIKE PROTEIN
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Gene: O174L
    Mutation: YES
    Organism Common: ASFV
    Organism Scientific: AFRICAN SWINE FEVER VIRUS
    Organism Taxid: 10497
    Synonym: PO174L, POLX
 
Molecule 2 - DNA (5'-D(*GP*TP*GP*AP*GP*TP*AP*CP*A)-3')
    Chains: F, C
    Engineered: YES
    Organism Scientific: SYNTHETIC CONSTRUCT
    Organism Taxid: 32630
    Synthetic: YES
 
Molecule 3 - DNA (5'- D(*CP*GP*TP*TP*CP*TP*AP*TP*GP*TP*GP*TP*AP*CP*TP*CP*AP*C)-3')
    Chains: H, E
    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: G, D
    Engineered: YES
    Organism Scientific: SYNTHETIC CONSTRUCT
    Organism Taxid: 32630
    Synthetic: YES

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 10)

Asymmetric Unit (3, 10)
No.NameCountTypeFull Name
1DGT2Ligand/Ion2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE
2MN4Ligand/IonMANGANESE (II) ION
3SO44Ligand/IonSULFATE ION
Biological Unit 1 (2, 3)
No.NameCountTypeFull Name
1DGT1Ligand/Ion2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE
2MN-1Ligand/IonMANGANESE (II) ION
3SO42Ligand/IonSULFATE ION
Biological Unit 2 (2, 3)
No.NameCountTypeFull Name
1DGT1Ligand/Ion2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE
2MN-1Ligand/IonMANGANESE (II) ION
3SO42Ligand/IonSULFATE ION

(-) Sites  (10, 10)

Asymmetric Unit (10, 10)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREGLY A:38 , SER A:39 , ARG A:42 , ASN A:48 , ASP A:49 , ASP A:51 , PHE A:115 , PHE A:116 , THR A:117 , GLY A:118 , VAL A:120 , MN A:202 , MN A:203 , DA F:9 , DG H:9binding site for residue DGT A 201
02AC2SOFTWAREASP A:49 , ASP A:51 , DGT A:201 , MN A:203 , HOH A:301binding site for residue MN A 202
03AC3SOFTWAREASP A:49 , ASP A:51 , ASP A:100 , DGT A:201 , MN A:202binding site for residue MN A 203
04AC4SOFTWARELYS A:109 , PRO A:110 , ILE A:113 , THR A:154 , THR A:155 , GLU A:156binding site for residue SO4 A 204
05AC5SOFTWARELYS A:136 , PHE A:143 , ASN A:145 , GLN A:146binding site for residue SO4 A 205
06AC6SOFTWAREGLY B:38 , SER B:39 , ARG B:42 , ASN B:48 , ASP B:49 , ASP B:51 , PHE B:116 , THR B:117 , GLY B:118 , VAL B:120 , MN B:202 , MN B:203 , DA C:9 , DG E:9binding site for residue DGT B 201
07AC7SOFTWARESER B:39 , ASP B:49 , ASP B:51 , DGT B:201 , MN B:203 , HOH B:301binding site for residue MN B 202
08AC8SOFTWAREASP B:49 , ASP B:51 , ASP B:100 , DGT B:201 , MN B:202 , DA C:9binding site for residue MN B 203
09AC9SOFTWARELYS B:109 , PRO B:110 , ILE B:113 , THR B:154 , THR B:155 , GLU B:156binding site for residue SO4 B 204
10AD1SOFTWAREPHE B:143 , GLN B:146 , THR B:147binding site for residue SO4 B 205

(-) SS Bonds  (2, 2)

Asymmetric Unit
No.Residues
1A:81 -A:86
2B:81 -B:86

(-) 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 5HRK)

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5HRK)

(-) 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:174
                                                                                                                                                                                                              
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eehhhhhhhhhhhh..eeee....eee.hhh.eeeehhhh....ee..eeeeeee.hhhhh......eee....eeeee....eeeeeeee..eeeeeeeeeee..hhhhhhhhhhhhhhhhhhhhhhhhhh..ee....eee..ee......hhhhhhhhhh....hhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5hrk A   1 MLTLIQGKKIVNHLRSRLAFEYNGQLIKILSKNIVAVGSLRREEKMLNDVDLLIIVPEKKLLKHVLPNIRIKGLSFSVKVCGERKCVLFIEWEKKTYQLDLFTALAEEKPYAIFFFTGPVSYLIRIRAALKKKNYKLNQYGLFKNQTLVPLKITTEKELIKELGFTYRIPKKRL 174
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170    


Chain B from PDB  Type:PROTEIN  Length:176
                                                                                                                                                                                                                
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eehhhhhhhhhhhh..eeee....eee.hhh.eeeehhhh....ee.eeeeeeee.hhhhhhhhh..eee................eeeee..eeeeeeeeeee..hhhhhhhhhhhhhhhhhhhhhhhhhh..ee....eee..ee......hhhhhhhhhh.......... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5hrk B  -1 GGMLTLIQGKKIVNHLRSRLAFEYNGQLIKILSKNIVAVGSLRREEKMLNDVDLLIIVPEKKLLKHVLPNIRIKGLSFSVKVCGERKCVLFIEWEKKTYQLDLFTALAEEKPYAIFFFTGPVSYLIRIRAALKKKNYKLNQYGLFKNQTLVPLKITTEKELIKELGFTYRIPKKRL 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:9
                                         
                 5hrk C   1 GTGAGTACA   9


Chain D from PDB  Type:DNA  Length:8
                                        
                 5hrk D   1 ATAGAACG   8


Chain E from PDB  Type:DNA  Length:18
                                                  
                 5hrk E   1 CGTTCTATGTGTACTCAC  18
                                    10        


Chain F from PDB  Type:DNA  Length:9
                                         
                 5hrk F   1 GTGAGTACA   9


Chain G from PDB  Type:DNA  Length:8
                                        
                 5hrk G   1 ATAGAACG   8


Chain H from PDB  Type:DNA  Length:18
                                                  
                 5hrk H   1 CGTTCTATGTGTACTCAC  18
                                    10
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  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 5HRK)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (0, 0)

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

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 Related Entries

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        A0A0A1E3N6_A | A0A0A1E3N6: 5hr9 5hrb 5hrd 5hre 5hrf 5hrg 5hrh 5hri 5hrl

(-) Related Entries Specified in the PDB File

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