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(-) Description

Title :  HUMAN TOPOISOMERASE IIBETA IN COMPLEX WITH DNA AND AMSACRINE
 
Authors :  C. C. Wu, T. K. Li, Y. C. Li, N. L. Chan
Date :  10 Jul 12  (Deposition) - 17 Jul 13  (Release) - 12 Mar 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.70
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-Isomerase Inhibitor 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: BL21 STAR (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
    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
    Synthetic: YES

 Structural Features

(-) Chains, Units

  123456
Asymmetric/Biological Unit : ABCDEF

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 8)

Asymmetric/Biological Unit (2, 8)
No.NameCountTypeFull Name
1ASW2Ligand/IonN-[4-(ACRIDIN-9-YLAMINO)-3-METHOXYPHENYL]METHANESULFONAMIDE
2MG6Ligand/IonMAGNESIUM ION

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:557 , ASP A:559 , HOH A:1401 , HOH A:1485 , HOH A:1549 , HOH C:102BINDING SITE FOR RESIDUE MG A 1301
2AC2SOFTWAREASN A:795 , ASN A:867 , HOH A:1559 , HOH A:1560 , HOH C:114BINDING SITE FOR RESIDUE MG A 1302
3AC3SOFTWAREPRO B:455 , ARG B:503 , GLY B:504 , LYS B:505 , ALA B:521 , GLU B:522 , GLN B:778 , DA D:12 , DG D:13 , DC E:8 , DT F:9BINDING SITE FOR RESIDUE ASW B 1301
4AC4SOFTWAREASP B:557 , ASP B:559 , HOH B:1412 , HOH B:1508 , HOH B:1554 , HOH E:107BINDING SITE FOR RESIDUE MG B 1302
5AC5SOFTWAREASN B:795 , HOH B:1568 , HOH B:1569 , HOH E:116 , HOH E:117BINDING SITE FOR RESIDUE MG B 1303
6AC6SOFTWAREDG D:17 , HOH D:219 , HOH D:220 , HOH D:221 , HOH D:222 , HOH E:113 , HOH E:114BINDING SITE FOR RESIDUE MG D 101
7AC7SOFTWAREPRO A:455 , ARG A:503 , GLY A:504 , LYS A:505 , ALA A:521 , GLU A:522 , DC C:8 , DT D:9 , DA F:12 , DG F:13 , HOH F:208BINDING SITE FOR RESIDUE ASW F 101
8AC8SOFTWAREHOH C:113 , HOH F:213 , HOH F:214 , HOH F:215 , HOH F:216 , HOH F:217BINDING SITE FOR RESIDUE MG F 102

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4G0U)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4G0U)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4G0U)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4G0U)

(-) Exons   (0, 0)

(no "Exon" information available for 4G0U)

(-) 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:655
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ............hhhh.eeeeeehhhhhhhhhhhh..hhhhheeeeee.....hhhhhhhhhhhhhhhhhhhhhhhh.........hhhhhh....eeeee...hhhhhhhhhhhhhhhhhhhhhhhhh..eeee.....eeeee..hhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhh..eeehhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhh....eehhhhhhhhhhhh....hhhhhhhhhhhhhh.................................ee....hhhhhhhhhhhhhh.eeee..eeeee.......hhhhhh..eee....eee....hhhhhhhhhhhhhh................eeeeee..eeeee.eeeeee..eeeeee.....hhhhhhhhhhhhhhhh.........eeee........eeee.hhhhhhhhhhhhhhhhh..eeeee....eee.....eee..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhh....hhhhhhhhh.....hhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4g0u A  455 PKLDDANDAGGKHSLECTLILTEGDSAKSLAVSGLGVIGRDRYGVFPLRGKILNVREASHKQIMENAEINNIIKIVGLQYKKSYDDAESLKTLRYGKIMIMTDQDQDGSHIKGLLINFIHHNWPSLLKHGFLEEFITERHRILFRYAGPEDDAAITLAFSKKKIDDRKEWLTNFMEDRRQRRLKHLTYNDFINKELILFSNSDNERSIPSLVDGFKPGQRKVLFTCFKRNDKREVKVAQLAGSVAEMSAYHHGEQALMMTIVNLAQNFVGSNNINLLQPIGQFGTRLHGGKDAASPRYIFTMLSTLARLLFPAVDDNLLKFLYDDNQRVEPEWYIPIIPMVLINGAEGIGTGWACKLPNYDAREIVNNVRRMLDGLDPHPMLPNYKNFKGTIQELGQNQYAVSGEIFVVDRNTVEITELPVRTWTQVYKEQVLEPMLNGTDKTPALISDYKEYHTDTTVKFVVKMTEEKLAQAEAAGLHKVFKLQTTLTCNSMVLFDHMGCLKKYETVQDILKEFFDLRLSYYGLRKEWLVGMLGAESTKLNNQARFILEKIQGKITIENRSKKDLIQMLVQRGYESDPVKAWKEAQEGPDFNYILNMSLWSLTKEKVEELIKQRDAKGREVNDLKRKSPSDLWKEDLAAFVEELDKVESQERED 1201
                                   464       474       484       494       504       514       524       534       544       554       564       574       584      |650       660       670       680       690  ||   713       723       733       743       753       763       773       783       793       803       813       823       833       843       853       863       873       883       893       903       913       923       933       943       953       963       973       983       993      1003      1013      1023      1033      1043      1053      1063      1073      1083      1093      1103      1136      1146      1156      1166      1176      1186      1196     
                                                                                                                                                                  591|                                          693|                                                                                                                                                                                                                                                                                                                                                                                                                1111|                                                                  
                                                                                                                                                                   648                                           707                                                                                                                                                                                                                                                                                                                                                                                                                 1135                                                                  


Chain B from PDB  Type:PROTEIN  Length:668
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..............hhhh.eeeeeehhhhhhhhhhhhhhhhh..eeeeee.....hhhhhhhhhhhhhhhhhhhhhhhh.........hhhhhhh...eeeee...hhhhhhhhhhhhhhhhhhhhhhhh...eeee..hhhhhhhhhhhhh.eeeee..hhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhh...eeehhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhh....eehhhhhhhhhhhhh...hhhhhhhhhhhhhh............................hhhh.ee....hhhhhhhhhhhhhh.eeee..eeeee.......hhhhhh..eee....eee....hhhhhhhhhhhhhh................eeeeee..eeeee.eeeeee..eeeeee.....hhhhhhhhhhhhhhhh.........eeee........eeee.hhhhhhhhhhhhhhhhh..eeeee...eeee.....eeee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhh....hhhhhhhhhh...hhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4g0u B  453 GIPKLDDANDAGGKHSLECTLILTEGDSAKSLAVSGLGVIGRDRYGVFPLRGKILNVREASHKQIMENAEINNIIKIVGLQYKKSYDDAESLKTLRYGKIMIMTDQDQDGSHIKGLLINFIHHNWPSLLKHGFLEEFITAKEAKEYFADMERHRILFRYAGPEDDAAITLAFSKKKIDDRKEWLTNFMEDRRQRRLTKHLTYNDFINKELILFSNSDNERSIPSLVDGFKPGQRKVLFTCFKRNDKREVKVAQLAGSVAEMSAYHHGEQALMMTIVNLAQNFVGSNNINLLQPIGQFGTRLHGGKDAASPRYIFTMLSTLARLLFPAVDDNLLKFLYDDNQRVEPEWYIPIIPMVLINGAEGIGTGWACKLPNYDAREIVNNVRRMLDGLDPHPMLPNYKNFKGTIQELGQNQYAVSGEIFVVDRNTVEITELPVRTWTQVYKEQVLEPMLNGTDKTPALISDYKEYHTDTTVKFVVKMTEEKLAQAEAAGLHKVFKLQTTLTCNSMVLFDHMGCLKKYETVQDILKEFFDLRLSYYGLRKEWLVGMLGAESTKLNNQARFILEKIQGKITIENRSKKDLIQMLVQRGYESDPVKAWKEAQGPDFNYILNMSLWSLTKEKVEELIKQRDAKGREVNDLKRKSPSDLWKEDLAAFVEELDKVESQERED 1201
                                   462       472       482       492       502       512       522       532       542       552       562       572       582       637       647       657       667       677       687     ||709       719       729       739       749       759       769       779       789       799       809       819       829       839       849       859       869       879       889       899       909       919       929       939       949       959       969       979       989       999      1009      1019      1029      1039      1049      1059      1069      1079      1089      1099      1109||    1143      1153      1163      1173      1183      1193        
                                                                                                                                                                   590|                                                      693|                                                                                                                                                                                                                                                                                                                                                                                                                1110|                                                                  
                                                                                                                                                                    636                                                       706                                                                                                                                                                                                                                                                                                                                                                                                                 1135                                                                  


Chain C from PDB  Type:DNA  Length:8
                                         
                4g0u C    1 AGCCGAGC    8


Chain D from PDB  Type:DNA  Length:12
                                             
                4g0u D    9 TGCAGCTCGGCT   20
                                    18  


Chain E from PDB  Type:DNA  Length:8
                                         
                4g0u E    1 AGCCGAGC    8


Chain F from PDB  Type:DNA  Length:12
                                             
                4g0u F    9 TGCAGCTCGGCT   20
                                    18
   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 4G0U)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4G0U)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4G0U)

(-) Gene Ontology  (33, 33)

Asymmetric/Biological Unit(hide GO term definitions)

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  4g0u
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  5.99.1.3
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 Related Entries

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

UniProtKB/Swiss-Prot
        TOP2B_HUMAN | Q02880: 3qx3 4g0v 4g0w 4j3n

(-) Related Entries Specified in the PDB File

3qx3 HUMAN TOPOISOMERASE IIBETA IN COMPLEX WITH DNA AND ETOPOSIDE
4g0v
4g0w
4j3n