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(-) Description

Title :  RE-REFINED HUMAN DNA TOPOISOMERASE IIA (ATPASE AND TRANSDUCER DOMAINS) IN COMPLEX WITH ADP AND SO4
 
Authors :  F. V. Stanger, T. Schirmer
Date :  05 Aug 14  (Deposition) - 24 Sep 14  (Release) - 05 Nov 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.51
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
Keywords :  Human Topoisomerase Iia, Isomerase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  F. V. Stanger, C. Dehio, T. Schirmer
Structure Of The N-Terminal Gyrase B Fragment In Complex With Adppi Reveals Rigid-Body Motion Induced By Atp Hydrolysis
Plos One V. 9 07289 2014
PubMed-ID: 25202966  |  Reference-DOI: 10.1371/JOURNAL.PONE.0107289
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - DNA TOPOISOMERASE 2-ALPHA
    Chains: A, B, C, D
    EC Number: 5.99.1.3
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PSB23
    Expression System Strain: ROSETTA(DE3)PLYSS
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 29-428
    Gene: TOP2, TOP2A
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: DNA TOPOISOMERASE II, ALPHA ISOZYME

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): AB  
Biological Unit 2 (1x):   CD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 12)

Asymmetric Unit (4, 12)
No.NameCountTypeFull Name
1ADP4Ligand/IonADENOSINE-5'-DIPHOSPHATE
2GOL1Ligand/IonGLYCEROL
3MG4Ligand/IonMAGNESIUM ION
4SO43Ligand/IonSULFATE ION
Biological Unit 1 (3, 4)
No.NameCountTypeFull Name
1ADP2Ligand/IonADENOSINE-5'-DIPHOSPHATE
2GOL1Ligand/IonGLYCEROL
3MG-1Ligand/IonMAGNESIUM ION
4SO41Ligand/IonSULFATE ION
Biological Unit 2 (2, 4)
No.NameCountTypeFull Name
1ADP2Ligand/IonADENOSINE-5'-DIPHOSPHATE
2GOL-1Ligand/IonGLYCEROL
3MG-1Ligand/IonMAGNESIUM ION
4SO42Ligand/IonSULFATE ION

(-) Sites  (12, 12)

Asymmetric Unit (12, 12)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASN A:91 , ADP A:502 , HOH A:601 , HOH A:633 , HOH A:635BINDING SITE FOR RESIDUE MG A 501
02AC2SOFTWAREASN A:91 , ASN A:95 , ARG A:98 , ASN A:120 , ILE A:125 , ILE A:141 , PHE A:142 , SER A:148 , SER A:149 , ASN A:150 , GLY A:161 , ARG A:162 , ASN A:163 , GLY A:164 , TYR A:165 , GLY A:166 , ALA A:167 , LYS A:168 , MG A:501 , HOH A:601 , HOH A:635 , TYR B:34BINDING SITE FOR RESIDUE ADP A 502
03AC3SOFTWARETYR A:50 , LYS A:83 , ASN A:163 , TYR A:165 , GLY A:166 , LYS A:378 , HOH A:635BINDING SITE FOR RESIDUE GOL A 503
04AC4SOFTWAREASN B:91 , ADP B:503 , HOH B:644 , HOH B:645 , HOH B:646BINDING SITE FOR RESIDUE MG B 501
05AC5SOFTWAREGLU B:87 , ARG B:162 , ASN B:163 , GLY B:164 , TYR B:165 , GLY B:166 , LYS B:378 , ADP B:503 , HOH B:645BINDING SITE FOR RESIDUE SO4 B 502
06AC6SOFTWARETYR A:34 , ASN B:91 , ASN B:95 , ASN B:120 , ILE B:125 , ILE B:141 , PHE B:142 , SER B:148 , SER B:149 , ASN B:150 , GLY B:161 , ARG B:162 , ASN B:163 , GLY B:164 , TYR B:165 , GLY B:166 , ALA B:167 , LYS B:168 , MG B:501 , SO4 B:502 , HOH B:603 , HOH B:606 , HOH B:612 , HOH B:645 , HOH B:646BINDING SITE FOR RESIDUE ADP B 503
07AC7SOFTWAREASN C:91 , ADP C:502 , HOH C:602 , HOH C:607 , HOH C:638BINDING SITE FOR RESIDUE MG C 501
08AC8SOFTWAREASN C:91 , ASN C:95 , ASN C:120 , ILE C:125 , ILE C:141 , PHE C:142 , SER C:148 , SER C:149 , ASN C:150 , GLY C:161 , ARG C:162 , ASN C:163 , GLY C:164 , TYR C:165 , GLY C:166 , ALA C:167 , LYS C:168 , MG C:501 , SO4 C:503 , HOH C:603 , HOH C:607 , HOH C:610 , HOH C:638 , TYR D:34BINDING SITE FOR RESIDUE ADP C 502
09AC9SOFTWAREGLU C:87 , ASN C:163 , TYR C:165 , GLY C:166 , LYS C:378 , ADP C:502 , HOH C:607BINDING SITE FOR RESIDUE SO4 C 503
10BC1SOFTWAREASN D:91 , ADP D:503 , HOH D:609 , HOH D:610 , HOH D:611BINDING SITE FOR RESIDUE MG D 501
11BC2SOFTWAREGLU D:87 , ARG D:162 , ASN D:163 , GLY D:164 , TYR D:165 , GLY D:166 , LYS D:378 , ADP D:503 , HOH D:611BINDING SITE FOR RESIDUE SO4 D 502
12BC3SOFTWARETYR C:34 , ASN D:91 , ASN D:95 , ASN D:120 , ILE D:125 , ILE D:141 , PHE D:142 , SER D:148 , SER D:149 , ASN D:150 , GLY D:161 , ARG D:162 , ASN D:163 , GLY D:164 , TYR D:165 , GLY D:166 , ALA D:167 , LYS D:168 , MG D:501 , SO4 D:502 , HOH D:610 , HOH D:611BINDING SITE FOR RESIDUE ADP D 503

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4R1F)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4R1F)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4R1F)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4R1F)

(-) Exons   (0, 0)

(no "Exon" information available for 4R1F)

(-) 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:366
                                                                                                                                                                                                                                                                                                                                                                                                              
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author hhhhhhee.hhhhhhhhhhhhhhh....eeeeeeeee...eeeeeeeeehhhhhhhhhhhhhhhhhhhhhh....eeeeeee....eeeeeee.......ee....eehhhhhhhh..ee...hhhhh........hhhhhhhhheeeeeeeeee....eeeeeeee....ee...eeee.....eeeeeeee.hhhhh....hhhhhhhhhhhhhhhhhhh...eeee..ee...hhhhhhhhhhh..eeeeee..eeeeeee.....eeeeee..ee...eehhhhhhhhhhhhhh...hhh.eeeeeee.............ee..hhhhh......hhhhhhhhhh..hhhhhhhh..eee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4r1f A  29 SVERIYQKKTQLEHILLRPDTYIGSVELVTQQMWVYDEDVGINYREVTFVPGLYKIFDEILVNAADNKQRDPKMSCIRVTIDPENNLISIWNNGKGIPVVEHKVEKMYVPALIFGQLLTSSNYDDDEKKVTGGRNGYGAKLCNIFSTKFTVETASREYKKMFKQTWMDNMGRAGEMELKPFNGEDYTCITFQPDLSKFKMQSLDKDIVALMVRRAYDIAGSTKDVKVFLNGNKLPVKGFRSYVDMYLKVIHEQVNHRWEVCLTMSEKGFQQISFVNSIATSKGGRHVDYVADQIVTKLVHQVKNHMWIFVNALIENPTFDSQTKENMTLQPKSFGSTCQLSEKFIKAAIGIVESILNWVKFKAQVQ 422
                                    38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       289       299       309       319       329       354       364       374       384       394       404|      416      
                                                                                                                                                                                                                                                                                 276|                                               338|                                               404|               
                                                                                                                                                                                                                                                                                  288                                                354                                                407               


Chain B from PDB  Type:PROTEIN  Length:379
                                                                                                                                                                                                                                                                                                                                                                                                                           
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhee.hhhhhhhhhhhhhhh....eeeeeeeee...eeeeeeeeehhhhhhhhhhhhhhhhhhhhhh....eeeeeee....eeeeeee.......ee....eehhhhhhhh..ee...hhhhh........hhhhhhhhheeeeeeeeeehhh.eeeeeeee....ee...eeee.....eeeeeeee.hhhhh....hhhhhhhhhhhhhhhhhhh...eeee..ee...hhhhhhhhhhh...eeeeee..eeeeeee.....eeeeee..ee...eehhhhhhhhhhhhhhhhhhhhh.hhhhhh.eeeeeee.............ee..hhhhh......hhhhhhhhhh..hhhhhhhhhhhhhhheee Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4r1f B  29 SVERIYQKKTQLEHILLRPDTYIGSVELVTQQMWVYDEDVGINYREVTFVPGLYKIFDEILVNAADNKQRDPKMSCIRVTIDPENNLISIWNNGKGIPVVEHKVEKMYVPALIFGQLLTSSNYDDDEKKVTGGRNGYGAKLCNIFSTKFTVETASREYKKMFKQTWMDNMGRAGEMELKPFNGEDYTCITFQPDLSKFKMQSLDKDIVALMVRRAYDIAGSTKDVKVFLNGNKLPVKGFRSYVDMYLKKVIHEQVNHRWEVCLTMSEKGFQQISFVNSIATSKGGRHVDYVADQIVTKLVDVVKKKKAHQVKNHMWIFVNALIENPTFDSQTKENMTLQPKSFGSTCQLSEKFIKAAIGCGIVESILNWVKFKAQVQLN 424
                                    38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       288       298       308       318       328       338     ||355       365       375       385       395       405       415         
                                                                                                                                                                                                                                                                                 276|                                                      344|                                                                        
                                                                                                                                                                                                                                                                                  287                                                       352                                                                        


Chain C from PDB  Type:PROTEIN  Length:384
                                                                                                                                                                                                                                                                                                                                                                                                                                
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .hhhhhee.hhhhhhhhhhhhhhh....eeeeeeeee...eeeeeeeeehhhhhhhhhhhhhhhhhhhhhh....eeeeeee....eeeeeee.......ee....eehhhhhhhh..ee.............hhhhhhhhheeeeeeeeeehhh.eeeeeeee....ee...eeee.....eeeeeeee.hhhhh....hhhhhhhhhhhhhhhhhhh...eeee..ee...hhhhhhhhhhh..eeeeee..eeeeeee.....eeeeee..ee....hhhhhhhhhhhhhhhhhhhhhhh......hhhhhhh.eeeeeee.................hhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhheeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4r1f C  29 SVERIYQKKTQLEHILLRPDTYIGSVELVTQQMWVYDEDVGINYREVTFVPGLYKIFDEILVNAADNKQRDPKMSCIRVTIDPENNLISIWNNGKGIPVVEHKVEKMYVPALIFGQLLTSSNYDDKVTGGRNGYGAKLCNIFSTKFTVETASREYKKMFKQTWMDNMGRAGEMELKPFNGEDYTCITFQPDLSKFKMQSLDKDIVALMVRRAYDIAGSTKDVKVFLNGNKLPVKGFRSYVDMYLKVIHEQVNHRWEVCLTMSEKGFQQISFVNSIATSKGGRHVDYVADQIVTKLVDVVKKKNKGGVAVKAHQVKNHMWIFVNALIENPTFDSQTKENMTLQPKSFGSTCQLSEKFIKAAIGCGIVESILNWVKFKAQVQLNKK 426
                                    38        48        58        68        78        88        98       108       118       128       138       148    || 161       171       181       191       201       211       221       231       241       251       261       271   ||  292       302       312       322       332       342       352       362       372       382       392       402       412       422    
                                                                                                                                                      153|                                                                                                                   275|                                                                                                                                           
                                                                                                                                                       157                                                                                                                    287                                                                                                                                           


Chain D from PDB  Type:PROTEIN  Length:373
                                                                                                                                                                                                                                                                                                                                                                                                                     
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhee.hhhhhhhhhhhhhhh....eeeeeeeee...eeeeeeeeehhhhhhhhhhhhhhhhhhhhhh....eeeeeee....eeeeeee.......ee....eehhhhhhhh..ee...hhhhh........hhhhhhhhheeeeeeeeeehhh.eeeeeeee....ee...eeee.....eeeeeeee.hhhhh....hhhhhhhhhhhhhhhhhhh...eeee..ee....hhhhhhhhhh...eeeeee..eeeeeee.....eeeeee..ee....hhhhhhhhhhhhhhhhhhh..hhhhhh.eeeeeee.................hhhhh......hhhhhhhhhhh....hhhhhheeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4r1f D  29 SVERIYQKKTQLEHILLRPDTYIGSVELVTQQMWVYDEDVGINYREVTFVPGLYKIFDEILVNAADNKQRDPKMSCIRVTIDPENNLISIWNNGKGIPVVEHKVEKMYVPALIFGQLLTSSNYDDDEKKVTGGRNGYGAKLCNIFSTKFTVETASREYKKMFKQTWMDNMGRAGEMELKPFNGEDYTCITFQPDLSKFKMQSLDKDIVALMVRRAYDIAGSTKDVKVFLNGNKLPVKGFRSYVDMYLKKVIHEQVNHRWEVCLTMSEKGFQQISFVNSIATSKGGRHVDYVADQIVTKLVDVVKKAHQVKNHMWIFVNALIENPTFDSQTKENMTLQPKSFGSTCQLSEKFIKAAIGCGIVWVKFKAQVQLNK 425
                                    38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       288       298       308       318       328       338   ||  357       367       377       387       397       407||     422   
                                                                                                                                                                                                                                                                                 276|                                                    342|                                                     408|           
                                                                                                                                                                                                                                                                                  287                                                     352                                                      414
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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 4R1F)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4R1F)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4R1F)

(-) Gene Ontology  (52, 52)

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 Related Entries

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

UniProtKB/Swiss-Prot
        TOP2A_HUMAN | P11388: 1lwz 1zxm 1zxn 4fm9

(-) Related Entries Specified in the PDB File

1ei1
1zxm
1zxn HUMAN DNA TOPOISOMERASE IIA ATPASE/ADP, THIS ENTRY 4R1F REFLECTS AN ALTERNATIVE MODELING OF X-RAY DATA R1ZXNSF.
4prv
4prx
4pu9