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(-) Description

Title :  HUMAN TOPOISOMERASE IIBETA IN COMPLEX WITH DNA AND MITOXANTRONE
 
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 :  2.55
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: 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
    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
1MG6Ligand/IonMAGNESIUM ION
2MIX2Ligand/Ion1,4-DIHYDROXY-5,8-BIS({2-[(2-HYDROXYETHYL)AMINO]ETHYL}AMINO)-9,10-ANTHRACENEDIONE

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:503 , GLY A:504 , LYS A:505 , ILE A:506 , ASN A:520 , GLU A:522 , GLN A:778 , MET A:782 , DC C:8 , DT D:9 , DA F:12 , DG F:13 , DC F:14BINDING SITE FOR RESIDUE MIX A 1301
2AC2SOFTWAREASP A:557 , ASP A:559BINDING SITE FOR RESIDUE MG A 1302
3AC3SOFTWAREASN A:795 , ASN A:867BINDING SITE FOR RESIDUE MG A 1303
4AC4SOFTWAREASP B:557 , ASP B:559BINDING SITE FOR RESIDUE MG B 1301
5AC5SOFTWAREASN B:795 , ASN B:867BINDING SITE FOR RESIDUE MG B 1302
6AC6SOFTWAREARG B:503 , GLY B:504 , LYS B:505 , ASN B:520 , GLU B:522 , GLN B:778 , DA D:12 , DG D:13 , DC D:14 , DC E:8 , DT F:9BINDING SITE FOR RESIDUE MIX D 101

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4G0V)

(-) 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 4G0V)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4G0V)

(-) Exons   (0, 0)

(no "Exon" information available for 4G0V)

(-) 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:663
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...............hhhh.eeeeeehhhhhhhhhhhhhhhhhh.eeeeee.....hhhhhhhhhhhhhhhhhhhhhhhh..........hhhhh....eeeee...hhhhhhhhhhhhhhhhhhhhhhhhh..eeee.......eeeee..hhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhh...eeehhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhh....eehhhhhhhhhhhhh...hhhhhhhhhhhhhh.................................ee....hhhhhhhhhhhhhh.eee....eeee.......hhhhhh.eeee....eeee...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
                4g0v A  452 KGIPKLDDANDAGGKHSLECTLILTEGDSAKSLAVSGLGVIGRDRYGVFPLRGKILNVREASHKQIMENAEINNIIKIVGLQYKKSYDDAESLKTLRYGKIMIMTDQDQDGSHIKGLLINFIHHNWPSLLKHGFLEEFITDMERHRILFRYAGPEDDAAITLAFSKKKIDDRKEWLTNFMEDRRQRRLHGLKHLTYNDFINKELILFSNSDNERSIPSLVDGFKPGQRKVLFTCFKRNDKREVKVAQLAGSVAEMSAYHHGEQALMMTIVNLAQNFVGSNNINLLQPIGQFGTRLHGGKDAASPRYIFTMLSTLARLLFPAVDDNLLKFLYDDNQRVEPEWYIPIIPMVLINGAEGIGTGWACKLPNYDAREIVNNVRRMLDGLDPHPMLPNYKNFKGTIQELGQNQYAVSGEIFVVDRNTVEITELPVRTWTQVYKEQVLEPMLNGTDKTPALISDYKEYHTDTTVKFVVKMTEEKLAQAEAAGLHKVFKLQTTLTCNSMVLFDHMGCLKKYETVQDILKEFFDLRLSYYGLRKEWLVGMLGAESTKLNNQARFILEKIQGKITIENRSKKDLIQMLVQRGYESDPVKAWKEAQEGPDFNYILNMSLWSLTKEKVEELIKQRDAKGREVNDLKRKSPSDLWKEDLAAFVEELDKVESQERED 1201
                                   461       471       481       491       501       511       521       531       541       551       561       571       581       591|      655       665       675       685       695||     715       725       735       745       755       765       775       785       795       805       815       825       835       845       855       865       875       885       895       905       915       925       935       945       955       965       975       985       995      1005      1015      1025      1035      1045      1055      1065      1075      1085      1095      1105     |1138      1148      1158      1168      1178      1188      1198   
                                                                                                                                                                     591|                                               696|                                                                                                                                                                                                                                                                                                                                                                                                                1111|                                                                  
                                                                                                                                                                      646                                                707                                                                                                                                                                                                                                                                                                                                                                                                                 1135                                                                  


Chain B from PDB  Type:PROTEIN  Length:666
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..................hhhh.eeeeeehhhhhhhhhhhhh.hhhh.eeeeee..........hhhhhhhhhhhhhhhhhhh..........hhhhhh...eeeee...hhhhhhhhhhhhhhhhhhhhhhhhh..eeee...hhhhhh.hhhh.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.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhh....hhhhhhhhhh...hhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                4g0v B  449 SKIKGIPKLDDANDAGGKHSLECTLILTEGDSAKSLAVSGLGVIGRDRYGVFPLRGKILNVREASHKQIMENAEINNIIKIVGLQYKKSYDDAESLKTLRYGKIMIMTDQDQDGSHIKGLLINFIHHNWPSLLKHGFLEEFIAKEAKEYFADMERHRILFRYAGPEDDAAITLAFSKKKIDDRKEWLTNFMEDRRQRRLKHLTYNDFINKELILFSNSDNERSIPSLVDGFKPGQRKVLFTCFKRNDKREVKVAQLAGSVAEMSAYHHGEQALMMTIVNLAQNFVGSNNINLLQPIGQFGTRLHGGKDAASPRYIFTMLSTLARLLFPAVDDNLLKFLYDDNQRVEPEWYIPIIPMVLINGAEGIGTGWACKLPNYDAREIVNNVRRMLDGLDPHPMLPNYKNFKGTIQELGQNQYAVSGEIFVVDRNTVEITELPVRTWTQVYKEQVLEPMLNGPALISDYKEYHTDTTVKFVVKMTEEKLAQAEAAGLHKVFKLQTTLTCNSMVLFDHMGCLKKYETVQDILKEFFDLRLSYYGLRKEWLVGMLGAESTKLNNQARFILEKIQGKITIENRSKKDLIQMLVQRGYESDPVKAWKEAQGPDFNYILNMSLWSLTKEKVEELIKQRDAKGREVNDLKRKSPSDLWKEDLAAFVEELDKVESQERED 1201
                                   458       468       478       488       498       508       518       528       538       548       558       568       578       588 ||    644       654       664       674       684       707       717       727       737       747       757       767       777       787       797       807       817       827       837       847       857       867       877       887       897       907       917       927       937       947       957    || 971       981       991      1001      1011      1021      1031      1041      1051      1061      1071      1081      1091      1101      1135      1145      1155      1165      1175      1185      1195      
                                                                                                                                                                       590|                                                     693|                                                                                                                                                                                                                                                            962|                                                                                                                                           1110|                                                                  
                                                                                                                                                                        637                                                      707                                                                                                                                                                                                                                                             967                                                                                                                                            1135                                                                  


Chain C from PDB  Type:DNA  Length:8
                                         
                4g0v C    1 AGCCGAGC    8


Chain D from PDB  Type:DNA  Length:12
                                             
                4g0v D    9 TGCAGCTCGGCT   20
                                    18  


Chain E from PDB  Type:DNA  Length:8
                                         
                4g0v E    1 AGCCGAGC    8


Chain F from PDB  Type:DNA  Length:12
                                             
                4g0v 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 4G0V)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4G0V)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4G0V)

(-) 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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  4g0v
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  TOP2B_HUMAN | Q02880
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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 4g0w 4j3n

(-) Related Entries Specified in the PDB File

3qx3 HUMAN TOPOISOMERASE IIBETA IN COMPLEX WITH DNA AND ETOPOSIDE
4g0u
4g0w
4j3n