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(-) Description

Title :  HUMAN TOPOISOMERASE IIBETA IN COMPLEX WITH DNA AND AMETANTRONE
 
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
1AKE2Ligand/Ion1,4-BIS({2-[(2-HYDROXYETHYL)AMINO]ETHYL}AMINO)ANTHRACENE-9,10-DIONE
2MG6Ligand/IonMAGNESIUM ION

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:557 , ASP A:559BINDING SITE FOR RESIDUE MG A 1301
2AC2SOFTWAREASN A:867 , GLY A:868BINDING SITE FOR RESIDUE MG A 1302
3AC3SOFTWAREASP B:557 , ASP B:559BINDING SITE FOR RESIDUE MG B 1301
4AC4SOFTWAREASN B:867BINDING SITE FOR RESIDUE MG B 1302
5AC5SOFTWAREARG B:503 , GLY B:504 , LYS B:505 , LEU B:507 , ASN B:520 , GLU B:522 , GLN B:778 , MET B:782 , DA D:12 , DG D:13 , DC D:14 , DG E:7 , DC E:8 , DT F:9BINDING SITE FOR RESIDUE AKE D 101
6AC6SOFTWAREDG D:18BINDING SITE FOR RESIDUE MG D 102
7AC7SOFTWAREARG A:503 , LYS A:505 , ILE A:506 , ASN A:520 , GLU A:522 , GLN A:778 , MET A:782 , DG C:7 , DC C:8 , DT D:9 , DA F:12 , DG F:13 , DC F:14BINDING SITE FOR RESIDUE AKE F 101
8AC8SOFTWAREDG F:17BINDING SITE FOR RESIDUE MG F 102

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4G0W)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4G0W)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4G0W)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4G0W)

(-) Exons   (0, 0)

(no "Exon" information available for 4G0W)

(-) 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:664
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...............hhhh.eeeeeehhhhhhhhhhhhhhhhhh.eeeeee.....hhhhhhhhhhhhhhhhhhhhhhhh...........hhhhh...eeeee...hhhhhhhhhhhhhhhhhhhhhhhhh..eeee...hhhhheeeee...hhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhh...eeehhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhh....eehhhhhhhhhhhh....hhhhhhhhhhhhhh.................................ee....hhhhhhhhhhhhhh.eee....eeee.......hhhhhh..eee....eee....hhhhhhhhhhhhhh................eeeeee..eeeee.eeeeee..eeeeee.....hhhhhhhhhhhhhhhh.........eeee........eeee.hhhhhhhhhhhhhhhhh..eeeee....eee.....eee..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhh....hhhhhhhhh.....hhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4g0w A  452 KGIPKLDDANDAGGKHSLECTLILTEGDSAKSLAVSGLGVIGRDRYGVFPLRGKILNVREASHKQIMENAEINNIIKIVGLQYKKSYDDAESLKTLRYGKIMIMTDQDQDGSHIKGLLINFIHHNWPSLLKHGFLEEFITADMERHRILFRYAGPEDDAAITLAFSKKKIDDRKEWLTNFMEDRRQRRLHGLKHLTYNDFINKELILFSNSDNERSIPSLVDGFKPGQRKVLFTCFKRNDKREVKVAQLAGSVAEMSAYHHGEQALMMTIVNLAQNFVGSNNINLLQPIGQFGTRLHGGKDAASPRYIFTMLSTLARLLFPAVDDNLLKFLYDDNQRVEPEWYIPIIPMVLINGAEGIGTGWACKLPNYDAREIVNNVRRMLDGLDPHPMLPNYKNFKGTIQELGQNQYAVSGEIFVVDRNTVEITELPVRTWTQVYKEQVLEPMLNGTDKTPALISDYKEYHTDTTVKFVVKMTEEKLAQAEAAGLHKVFKLQTTLTCNSMVLFDHMGCLKKYETVQDILKEFFDLRLSYYGLRKEWLVGMLGAESTKLNNQARFILEKIQGKITIENRSKKDLIQMLVQRGYESDPVKAWKEAQEGPDFNYILNMSLWSLTKEKVEELIKQRDAKGREVNDLKRKSPSDLWKEDLAAFVEELDKVESQERED 1201
                                   461       471       481       491       501       511       521       531       541       551       561       571       581       591|      654       664       674       684       694 ||    714       724       734       744       754       764       774       784       794       804       814       824       834       844       854       864       874       884       894       904       914       924       934       944       954       964       974       984       994      1004      1014      1024      1034      1044      1054      1064      1074      1084      1094      1104      1137      1147      1157      1167      1177      1187      1197    
                                                                                                                                                                     591|                                                696|                                                                                                                                                                                                                                                                                                                                                                                                                1111|                                                                  
                                                                                                                                                                      645                                                 707                                                                                                                                                                                                                                                                                                                                                                                                                 1135                                                                  


Chain B from PDB  Type:PROTEIN  Length:664
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..................hhhh.eeeeeehhhhhhhhhhhhh.hhhh.eeeeee..........hhhhhhhhhhhhhhhhhhh..........hhhhhh...eeeee...hhhhhhhhhhhhhhhhhhhhhhhhh..eeee.....hhhh.eeeee..hhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhh...eeehhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhh....eehhhhhhhhhhhhh...hhhhhhhhhhhhhh.................................ee....hhhhhhhhhhhhhh.eee....eeee.......hhhhhh..eee....eee....hhhhhhhhhhhhhh................eeeeee..eeeee.eeeeee..eeeeee.....hhhhhhhhhhhhhhh......eeee........eeee.hhhhhhhhhhhhhhhhh..eeeee...eeee.....eeee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhh....hhhhhhhhh....hhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4g0w B  449 SKIKGIPKLDDANDAGGKHSLECTLILTEGDSAKSLAVSGLGVIGRDRYGVFPLRGKILNVREASHKQIMENAEINNIIKIVGLQYKKSYDDAESLKTLRYGKIMIMTDQDQDGSHIKGLLINFIHHNWPSLLKHGFLEEFITPFADMERHRILFRYAGPEDDAAITLAFSKKKIDDRKEWLTNFMEDRRQRRLHGTKHLTYNDFINKELILFSNSDNERSIPSLVDGFKPGQRKVLFTCFKRNDKREVKVAQLAGSVAEMSAYHHGEQALMMTIVNLAQNFVGSNNINLLQPIGQFGTRLHGGKDAASPRYIFTMLSTLARLLFPAVDDNLLKFLYDDNQRVEPEWYIPIIPMVLINGAEGIGTGWACKLPNYDAREIVNNVRRMLDGLDPHPMLPNYKNFKGTIQELGQNQYAVSGEIFVVDRNTVEITELPVRTWTQVYKEQVLEPMLNGPALISDYKEYHTDTTVKFVVKMTEEKLAQAEAAGLHKVFKLQTTLTCNSMVLFDHMGCLKKYETVQDILKEFFDLRLSYYGLRKEWLVGMLGAESTKLNNQARFILEKIQGKITIENRSKKDLIQMLVQRGYESDPVKAWKEAQGPDFNYILNMSLWSLTKEKVEELIKQRDAKGREVNDLKRKSPSDLWKEDLAAFVEELDKVESQERED 1201
                                   458       468       478       488       498       508       518       528       538       548       558       568       578       588   ||  649       659       669       679       689     ||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  ||   973       983       993      1003      1013      1023      1033      1043      1053      1063      1073      1083      1093      1103      1137      1147      1157      1167      1177      1187      1197    
                                                                                                                                                                         592|                                                695|                                                                                                                                                                                                                                                             962|                                                                                                                                           1110|                                                                  
                                                                                                                                                                          644                                                 706                                                                                                                                                                                                                                                              967                                                                                                                                            1135                                                                  


Chain C from PDB  Type:DNA  Length:8
                                         
                4g0w C    1 AGCCGAGC    8


Chain D from PDB  Type:DNA  Length:12
                                             
                4g0w D    9 TGCAGCTCGGCT   20
                                    18  


Chain E from PDB  Type:DNA  Length:8
                                         
                4g0w E    1 AGCCGAGC    8


Chain F from PDB  Type:DNA  Length:12
                                             
                4g0w 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 4G0W)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4G0W)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4G0W)

(-) Gene Ontology  (33, 33)

Asymmetric/Biological Unit(hide GO term definitions)

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  4g0w
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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 4g0u 4g0v 4j3n

(-) Related Entries Specified in the PDB File

3qx3 HUMAN TOPOISOMERASE IIBETA IN COMPLEX WITH DNA AND ETOPOSIDE
4g0u
4g0v
4j3n