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(-) Description

Title :  HUMAN TOPOISOMERASE IIBETA IN COMPLEX WITH DNA
 
Authors :  C. C. Wu, T. K. Li, Y. C. Li, N. L. Chan
Date :  06 Feb 13  (Deposition) - 02 Oct 13  (Release) - 19 Mar 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym./Biol. Unit :  A,B,C,D,E,F
Keywords :  Toprim Domain, Winged-Helix Domain, Coiled-Coil Domain, Dna Binding And Cleavage, Nucleus, Isomerase-Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  C. C. Wu, Y. C. Li, Y. R. Wang, T. K. Li, N. L. Chan
On The Structural Basis And Design Guidelines For Type Ii Topoisomerase-Targeting Anticancer Drugs
Nucleic Acids Res. V. 41 10630 2013
PubMed-ID: 24038465  |  Reference-DOI: 10.1093/NAR/GKT828

(-) Compounds

Molecule 1 - DNA TOPOISOMERASE 2-BETA
    Chains: A, B
    EC Number: 5.99.1.3
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET51B
    Expression System Strain: BL21STAR(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: HTOP2BETA CLEAVAGE CORE, UNP RESIDUES 450-1206
    Gene: TOP2B
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: DNA TOPOISOMERASE II, BETA ISOZYME
 
Molecule 2 - DNA (5'-D(P*AP*GP*CP*CP*GP*AP*GP*C)-3')
    Chains: C, E
    Engineered: YES
    Other Details: THE OLIGONUCLEOTIDE SEQUENCE 5'-AGCCGAGCTGCAGCTCGGCT- 3' WAS ORDERED FROM VIOGENE.
    Synthetic: YES
 
Molecule 3 - DNA (5'-D(P*TP*GP*CP*AP*GP*CP*TP*CP*GP*GP*CP*T)-3')
    Chains: D, F
    Engineered: YES
    Other Details: THE OLIGONUCLEOTIDE SEQUENCE 5'-AGCCGAGCTGCAGCTCGGCT- 3' WAS ORDERED FROM VIOGENE.
    Synthetic: YES

 Structural Features

(-) Chains, Units

  123456
Asymmetric/Biological Unit : ABCDEF

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 7)

Asymmetric/Biological Unit (1, 7)
No.NameCountTypeFull Name
1MG7Ligand/IonMAGNESIUM ION

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:557 , ASP A:559 , HOH A:1401 , HOH A:1614 , HOH A:1615 , HOH C:103BINDING SITE FOR RESIDUE MG A 1301
2AC2SOFTWAREASN A:867 , GLY A:868 , HOH A:1624 , HOH C:122 , HOH C:123BINDING SITE FOR RESIDUE MG A 1302
3AC3SOFTWAREPHE A:722 , ASP A:726 , HOH A:1430 , DC F:16 , HOH F:213BINDING SITE FOR RESIDUE MG A 1303
4AC4SOFTWAREASP B:557 , ASP B:559 , HOH B:1402 , HOH B:1434 , HOH B:1516 , HOH B:1672BINDING SITE FOR RESIDUE MG B 1301
5AC5SOFTWAREASN B:795 , ASN B:867 , HOH B:1679 , HOH B:1680 , HOH E:124 , HOH E:125BINDING SITE FOR RESIDUE MG B 1302
6AC6SOFTWAREHOH B:1612 , HOH B:1740 , HOH D:202 , HOH D:203 , HOH D:208BINDING SITE FOR RESIDUE MG D 101
7AC7SOFTWAREHOH A:1626 , HOH A:1627 , HOH F:214 , HOH F:215 , HOH F:216BINDING SITE FOR RESIDUE MG F 101

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4J3N)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Gly A:490 -Val A:491

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4J3N)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4J3N)

(-) Exons   (0, 0)

(no "Exon" information available for 4J3N)

(-) Sequences/Alignments

Asymmetric/Biological 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:666
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ............hhhh.eeeeeehhhhhhhhhhhhhhhhhh.eeeeee..........hhhhhhhhhhhhhhhhhhh...........hhhhh...eeeee...hhhhhhhhhhhhhhhhhhhhhhhhh..eeee...hhhhhhhhh.eeeee..hhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhh.....eeehhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhh....eehhhhhhhhhhhhh...hhhhhhhhhhhhhh............................hhhh.ee....hhhhhhhhhhhh...eeee..eeeee.......hhhhhh..eee....eee....hhhhhhhhhhhhhh................eeeeee..eeeee.eeeeee..eeeeee.....hhhhhhhhhhhhhhhh.........eeee........eeee.hhhhhhhhhhhhhhhhh..eeeee...eeee.....eeee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhh....hhhhhhhhhh....hhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                4j3n A  455 PKLDDANDAGGKHSLECTLILTEGDSAKSLAVSGLGVIGRDRYGVFPLRGKILNVREASHKQIMENAEINNIIKIVGLQYKKSYDDAESLKTLRYGKIMIMTDQDQDGSHIKGLLINFIHHNWPSLLKHGFLEEFITAKEYFADMERHRILFRYAGPEDDAAITLAFSKKKIDDRKEWLTNFMEDRRQRRLHGLKHLTYNDFINKELILFSNSDNERSIPSLVDGFKPGQRKVLFTCFKRNDKREVKVAQLAGSVAEMSAYHHGEQALMMTIVNLAQNFVGSNNINLLQPIGQFGTRLHGGKDAASPRYIFTMLSTLARLLFPAVDDNLLKFLYDDNQRVEPEWYIPIIPMVLINGAEGIGTGWACKLPNYDAREIVNNVRRMLDGLDPHPMLPNYKNFKGTIQELGQNQYAVSGEIFVVDRNTVEITELPVRTWTQVYKEQVLEPMLNGTDKTPALISDYKEYHTDTTVKFVVKMTEEKLAQAEAAGLHKVFKLQTTLTCNSMVLFDHMGCLKKYETVQDILKEFFDLRLSYYGLRKEWLVGMLGAESTKLNNQARFILEKIQGKITIENRSKKDLIQMLVQRGYESDPVKAWKEAQEGPDFNYILNMSLWSLTKEKVEELIKQRDAKGREVNDLKRKSPSDLWKEDLAAFVEELDKVESQERED 1201
                                   464       474       484       494       504       514       524       534       544       554       564       574       584      |642       652       662       672       682       692   ||  712       722       732       742       752       762       772       782       792       802       812       822       832       842       852       862       872       882       892       902       912       922       932       942       952       962       972       982       992      1002      1012      1022      1032      1042      1052      1062      1072      1082      1092      1102      1135      1145      1155      1165      1175      1185      1195      
                                                                                                                                                                  591|                                                     696|                                                                                                                                                                                                                                                                                                                                                                                                                1111|                                                                  
                                                                                                                                                                   640                                                      707                                                                                                                                                                                                                                                                                                                                                                                                                 1135                                                                  


Chain B from PDB  Type:PROTEIN  Length:670
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..................hhhh.eeeeeehhhhhhhhhhhhhhhhhh.eeeeee..........hhhhhhhhhhhhhhhhhhh..........hhhhhh...eeeee...hhhhhhhhhhhhhhhhhhhhhhhh...eeee....hhhhhhhhhhhh.eeeee..hhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhh.....eeehhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhh....eehhhhhhhhhhhhh...hhhhhhhhhhhhhh.................................ee....hhhhhhhhhhhhhh.eeee..eeeee.......hhhhhh..eee....eee....hhhhhhhhhhhhhh................eeeeee..eeeee.eeeeee..eeeeee.....hhhhhhhhhhhhhhh.....eeee........eeee.hhhhhhhhhhhhhhhhh..eeeee...eeee.....eeee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhh....hhhhhhhhhh...hhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4j3n B  449 SKIKGIPKLDDANDAGGKHSLECTLILTEGDSAKSLAVSGLGVIGRDRYGVFPLRGKILNVREASHKQIMENAEINNIIKIVGLQYKKSYDDAESLKTLRYGKIMIMTDQDQDGSHIKGLLINFIHHNWPSLLKHGFLEEFITPAKEAKEYFADMERHRILFRYAGPEDDAAITLAFSKKKIDDRKEWLTNFMEDRRQRRLHGTKHLTYNDFINKELILFSNSDNERSIPSLVDGFKPGQRKVLFTCFKRNDKREVKVAQLAGSVAEMSAYHHGEQALMMTIVNLAQNFVGSNNINLLQPIGQFGTRLHGGKDAASPRYIFTMLSTLARLLFPAVDDNLLKFLYDDNQRVEPEWYIPIIPMVLINGAEGIGTGWACKLPNYDAREIVNNVRRMLDGLDPHPMLPNYKNFKGTIQELGQNQYAVSGEIFVVDRNTVEITELPVRTWTQVYKEQVLEPMLNPALISDYKEYHTDTTVKFVVKMTEEKLAQAEAAGLHKVFKLQTTLTCNSMVLFDHMGCLKKYETVQDILKEFFDLRLSYYGLRKEWLVGMLGAESTKLNNQARFILEKIQGKITIENRSKKDLIQMLVQRGYESDPVKAWKEAQGPDFNYILNMSLWSLTKEKVEELIKQRDAKGREVNDLKRKSPSDLWKEDLAAFVEELDKVESQERED 1201
                                   458       468       478       488       498       508       518       528       538       548       558       568       578       588   ||  642       652       662       672       682       692  ||   712       722       732       742       752       762       772       782       792       802       812       822       832       842       852       862       872       882       892       902       912       922       932       942       952       967       977       987       997      1007      1017      1027      1037      1047      1057      1067      1077      1087      1097      1107  ||  1141      1151      1161      1171      1181      1191      1201
                                                                                                                                                                         592|                                                       695|                                                                                                                                                                                                                                                            961|                                                                                                                                           1110|                                                                  
                                                                                                                                                                          637                                                        706                                                                                                                                                                                                                                                             967                                                                                                                                            1135                                                                  


Chain C from PDB  Type:DNA  Length:8
                                         
                4j3n C    1 AGCCGAGC    8


Chain D from PDB  Type:DNA  Length:12
                                             
                4j3n D    9 TGCAGCTCGGCT   20
                                    18  


Chain E from PDB  Type:DNA  Length:8
                                         
                4j3n E    1 AGCCGAGC    8


Chain F from PDB  Type:DNA  Length:11
                                            
                4j3n F    9 TGCGCTCGGCT   20
                              ||    19 
                             11|       
                              13
   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 4J3N)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4J3N)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4J3N)

(-) Gene Ontology  (33, 33)

Asymmetric/Biological Unit(hide GO term definitions)

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  Cis Peptide Bonds
    Gly A:490 - Val A:491   [ RasMol ]  
 

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  4j3n
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 Related Entries

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

UniProtKB/Swiss-Prot
        TOP2B_HUMAN | Q02880: 3qx3 4g0u 4g0v 4g0w

(-) Related Entries Specified in the PDB File

3qx3 HUMAN TOPOISOMERASE IIBETA IN COMPLEX WITH DNA AND ETOPOSIDE
4g0u HUMAN TOPOISOMERASE IIBETA IN COMPLEX WITH DNA AND AMSACRINE
4g0v HUMAN TOPOISOMERASE IIBETA IN COMPLEX WITH DNA AND MITOXANTRONE
4g0w HUMAN TOPOISOMERASE IIBETA IN COMPLEX WITH DNA AND AMETANTRONE