eF-site ID 3qx3-ABCDEF
PDB Code 3qx3
Chain A, B, C, D, E, F

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Title Human topoisomerase IIbeta in complex with DNA and etoposide
Classification ISOMERASE/DNA/ISOMERASE INHIBITOR
Compound DNA topoisomerase 2-beta
Source Homo sapiens (Human) (3QX3)
Sequence A:  KGIPKLDDANDAGGKHSLECTLILTEGDSAKSLAVSGLGV
IGRDRYGVFPLRGKILNVREASHKQIMENAEINNIIKIVG
LQYKKSYDDAESLKTLRYGKIMIMTDQDQDGSHIKGLLIN
FIHHNWPSLLKHGFLEEFITKEAKEYFADMERHRILFRYA
GPEDDAAITLAFSKKKIDDRKEWLTNFMEDRRQRRLHGLK
HLTYNDFINKELILFSNSDNERSIPSLVDGFKPGQRKVLF
TCFKRNDKREVKVAQLAGSVAEMSAYHHGEQALMMTIVNL
AQNFVGSNNINLLQPIGQFGTRLHGGKDAASPRYIFTMLS
TLARLLFPAVDDNLLKFLYDDNQRVEPEWYIPIIPMVLIN
GAEGIGTGWACKLPNYDAREIVNNVRRMLDGLDPHPMLPN
YKNFKGTIQELGQNQYAVSGEIFVVDRNTVEITELPVRTW
TQVYKEQVLEPMLNGTDKTPALISDYKEYHTDTTVKFVVK
MTEEKLAQAEAAGLHKVFKLQTTLTCNSMVLFDHMGCLKK
YETVQDILKEFFDLRLSYYGLRKEWLVGMLGAESTKLNNQ
ARFILEKIQGKITIENRSKKDLIQMLVQRGYESDPVKAWK
EAQEGPDFNYILNMSLWSLTKEKVEELIKQRDAKGREVND
LKRKSPSDLWKEDLAAFVEELDKVESQERED
B:  SKIKGIPKLDDANDAGGKHSLECTLILTEGDSAKSLAVSG
LGVIGRDRYGVFPLRGKILNVREASHKQIMENAEINNIIK
IVGLQYKKSYDDAESLKTLRYGKIMIMTDQDQDGSHIKGL
LINFIHHNWPSLLKHGFLEEFITPAKEAKEYFADMERHRI
LFRYAGPEDDAAITLAFSKKKIDDRKEWLTNFMEDRRQRR
LHGTKHLTYNDFINKELILFSNSDNERSIPSLVDGFKPGQ
RKVLFTCFKRNDKREVKVAQLAGSVAEMSAYHHGEQALMM
TIVNLAQNFVGSNNINLLQPIGQFGTRLHGGKDAASPRYI
FTMLSTLARLLFPAVDDNLLKFLYDDNQRVEPEWYIPIIP
MVLINGAEGIGTGWACKLPNYDAREIVNNVRRMLDGLDPH
PMLPNYKNFKGTIQELGQNQYAVSGEIFVVDRNTVEITEL
PVRTWTQVYKEQVLEPMLNGPALISDYKEYHTDTTVKFVV
KMTEEKLAQAEAAGLHKVFKLQTTLTCNSMVLFDHMGCLK
KYETVQDILKEFFDLRLSYYGLRKEWLVGMLGAESTKLNN
QARFILEKIQGKITIENRSKKDLIQMLVQRGYESDPVKAW
KEAQGPDFNYILNMSLWSLTKEKVEELIKQRDAKGREVND
LKRKSPSDLWKEDLAAFVEELDKVESQERED
C:  AGCCGAGC
D:  TGCAGCTCGGCT
E:  AGCCGAGC
F:  TGCAGCTCGGCT
Description


Functional site

1) chain A
residue 478
type
sequence G
description BINDING SITE FOR RESIDUE EVP A 1
source : AC1

2) chain A
residue 479
type
sequence D
description BINDING SITE FOR RESIDUE EVP A 1
source : AC1

3) chain A
residue 503
type
sequence R
description BINDING SITE FOR RESIDUE EVP A 1
source : AC1

4) chain A
residue 778
type
sequence Q
description BINDING SITE FOR RESIDUE EVP A 1
source : AC1

5) chain A
residue 782
type
sequence M
description BINDING SITE FOR RESIDUE EVP A 1
source : AC1

6) chain C
residue 8
type
sequence C
description BINDING SITE FOR RESIDUE EVP A 1
source : AC1

7) chain D
residue 9
type
sequence T
description BINDING SITE FOR RESIDUE EVP A 1
source : AC1

8) chain D
residue 10
type
sequence G
description BINDING SITE FOR RESIDUE EVP A 1
source : AC1

9) chain F
residue 12
type
sequence A
description BINDING SITE FOR RESIDUE EVP A 1
source : AC1

10) chain F
residue 13
type
sequence G
description BINDING SITE FOR RESIDUE EVP A 1
source : AC1

11) chain A
residue 557
type
sequence D
description BINDING SITE FOR RESIDUE MG A 1222
source : AC2

12) chain A
residue 559
type
sequence D
description BINDING SITE FOR RESIDUE MG A 1222
source : AC2

13) chain A
residue 867
type
sequence N
description BINDING SITE FOR RESIDUE MG A 1223
source : AC3

14) chain A
residue 868
type
sequence G
description BINDING SITE FOR RESIDUE MG A 1223
source : AC3

15) chain A
residue 870
type
sequence E
description BINDING SITE FOR RESIDUE MG A 1223
source : AC3

16) chain B
residue 557
type
sequence D
description BINDING SITE FOR RESIDUE MG B 1
source : AC4

17) chain B
residue 559
type
sequence D
description BINDING SITE FOR RESIDUE MG B 1
source : AC4

18) chain B
residue 867
type
sequence N
description BINDING SITE FOR RESIDUE MG B 1222
source : AC5

19) chain B
residue 478
type
sequence G
description BINDING SITE FOR RESIDUE EVP D 1
source : AC6

20) chain B
residue 479
type
sequence D
description BINDING SITE FOR RESIDUE EVP D 1
source : AC6

21) chain B
residue 503
type
sequence R
description BINDING SITE FOR RESIDUE EVP D 1
source : AC6

22) chain B
residue 782
type
sequence M
description BINDING SITE FOR RESIDUE EVP D 1
source : AC6

23) chain D
residue 12
type
sequence A
description BINDING SITE FOR RESIDUE EVP D 1
source : AC6

24) chain D
residue 13
type
sequence G
description BINDING SITE FOR RESIDUE EVP D 1
source : AC6

25) chain E
residue 8
type
sequence C
description BINDING SITE FOR RESIDUE EVP D 1
source : AC6

26) chain F
residue 9
type
sequence T
description BINDING SITE FOR RESIDUE EVP D 1
source : AC6

27) chain F
residue 10
type
sequence G
description BINDING SITE FOR RESIDUE EVP D 1
source : AC6

28) chain B
residue 641
type CROSSLNK
sequence K
description Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2) => ECO:0007744|PubMed:28112733
source Swiss-Prot : SWS_FT_FI8

29) chain B
residue 671
type CROSSLNK
sequence K
description Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2) => ECO:0007744|PubMed:28112733
source Swiss-Prot : SWS_FT_FI8

30) chain B
residue 707
type CROSSLNK
sequence K
description Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2) => ECO:0007744|PubMed:28112733
source Swiss-Prot : SWS_FT_FI8

31) chain B
residue 1087
type CROSSLNK
sequence K
description Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2) => ECO:0007744|PubMed:28112733
source Swiss-Prot : SWS_FT_FI8

32) chain A
residue 641
type CROSSLNK
sequence K
description Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2) => ECO:0007744|PubMed:28112733
source Swiss-Prot : SWS_FT_FI8

33) chain A
residue 671
type CROSSLNK
sequence K
description Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2) => ECO:0007744|PubMed:28112733
source Swiss-Prot : SWS_FT_FI8

34) chain A
residue 707
type CROSSLNK
sequence K
description Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2) => ECO:0007744|PubMed:28112733
source Swiss-Prot : SWS_FT_FI8

35) chain A
residue 1087
type CROSSLNK
sequence K
description Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2) => ECO:0007744|PubMed:28112733
source Swiss-Prot : SWS_FT_FI8

36) chain A
residue 638
type CROSSLNK
sequence K
description Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2) => ECO:0007744|PubMed:25772364, ECO:0007744|PubMed:28112733
source Swiss-Prot : SWS_FT_FI9

37) chain B
residue 638
type CROSSLNK
sequence K
description Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2) => ECO:0007744|PubMed:25772364, ECO:0007744|PubMed:28112733
source Swiss-Prot : SWS_FT_FI9

38) chain A
residue 820
type SITE
sequence R
description Transition state stabilizer
source Swiss-Prot : SWS_FT_FI6

39) chain B
residue 820
type SITE
sequence R
description Transition state stabilizer
source Swiss-Prot : SWS_FT_FI6

40) chain A
residue 872
type SITE
sequence I
description Important for DNA bending; intercalates between base pairs of target DNA
source Swiss-Prot : SWS_FT_FI7

41) chain B
residue 872
type SITE
sequence I
description Important for DNA bending; intercalates between base pairs of target DNA
source Swiss-Prot : SWS_FT_FI7

42) chain A
residue 477
type BINDING
sequence E
description BINDING => ECO:0000255|PROSITE-ProRule:PRU00995
source Swiss-Prot : SWS_FT_FI2

43) chain B
residue 477
type BINDING
sequence E
description BINDING => ECO:0000255|PROSITE-ProRule:PRU00995
source Swiss-Prot : SWS_FT_FI2

44) chain A
residue 475-483
type prosite
sequence LTEGDSAKS
description TOPOISOMERASE_II DNA topoisomerase II signature. LTEGDSAKS
source prosite : PS00177

45) chain A
residue 557
type BINDING
sequence D
description BINDING => ECO:0000255|PROSITE-ProRule:PRU00995, ECO:0000269|PubMed:21778401
source Swiss-Prot : SWS_FT_FI3

46) chain A
residue 559
type BINDING
sequence D
description BINDING => ECO:0000255|PROSITE-ProRule:PRU00995, ECO:0000269|PubMed:21778401
source Swiss-Prot : SWS_FT_FI3

47) chain B
residue 557
type BINDING
sequence D
description BINDING => ECO:0000255|PROSITE-ProRule:PRU00995, ECO:0000269|PubMed:21778401
source Swiss-Prot : SWS_FT_FI3

48) chain B
residue 559
type BINDING
sequence D
description BINDING => ECO:0000255|PROSITE-ProRule:PRU00995, ECO:0000269|PubMed:21778401
source Swiss-Prot : SWS_FT_FI3

49) chain A
residue 505
type SITE
sequence K
description Interaction with DNA
source Swiss-Prot : SWS_FT_FI4

50) chain B
residue 678
type SITE
sequence K
description Interaction with DNA
source Swiss-Prot : SWS_FT_FI4

51) chain B
residue 739
type SITE
sequence K
description Interaction with DNA
source Swiss-Prot : SWS_FT_FI4

52) chain B
residue 947
type SITE
sequence W
description Interaction with DNA
source Swiss-Prot : SWS_FT_FI4

53) chain A
residue 508
type SITE
sequence N
description Interaction with DNA
source Swiss-Prot : SWS_FT_FI4

54) chain A
residue 677
type SITE
sequence R
description Interaction with DNA
source Swiss-Prot : SWS_FT_FI4

55) chain A
residue 678
type SITE
sequence K
description Interaction with DNA
source Swiss-Prot : SWS_FT_FI4

56) chain A
residue 739
type SITE
sequence K
description Interaction with DNA
source Swiss-Prot : SWS_FT_FI4

57) chain A
residue 947
type SITE
sequence W
description Interaction with DNA
source Swiss-Prot : SWS_FT_FI4

58) chain B
residue 505
type SITE
sequence K
description Interaction with DNA
source Swiss-Prot : SWS_FT_FI4

59) chain B
residue 508
type SITE
sequence N
description Interaction with DNA
source Swiss-Prot : SWS_FT_FI4

60) chain B
residue 677
type SITE
sequence R
description Interaction with DNA
source Swiss-Prot : SWS_FT_FI4

61) chain A
residue 773
type SITE
sequence Y
description Interaction with DNA => ECO:0000255|PROSITE-ProRule:PRU00995
source Swiss-Prot : SWS_FT_FI5

62) chain B
residue 773
type SITE
sequence Y
description Interaction with DNA => ECO:0000255|PROSITE-ProRule:PRU00995
source Swiss-Prot : SWS_FT_FI5

63) chain A
residue 821
type ACT_SITE
sequence Y
description O-(5'-phospho-DNA)-tyrosine intermediate => ECO:0000255|PROSITE-ProRule:PRU01384, ECO:0000269|PubMed:21778401
source Swiss-Prot : SWS_FT_FI1

64) chain B
residue 821
type ACT_SITE
sequence Y
description O-(5'-phospho-DNA)-tyrosine intermediate => ECO:0000255|PROSITE-ProRule:PRU01384, ECO:0000269|PubMed:21778401
source Swiss-Prot : SWS_FT_FI1


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