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SMTL ID : 1qzr.1
CRYSTAL STRUCTURE OF THE ATPASE REGION OF SACCHAROMYCES CEREVISIAE TOPOISOMERASE II BOUND TO ICRF-187 (DEXRAZOXANE)
Coordinates
PDB Format
Method
X-RAY DIFFRACTION 1.90 Å
Oligo State
homo-dimer
Ligands
2 x
MG
:
MAGNESIUM ION
(Non-covalent)
MG.1:
2 residues within 4Å:
Chain A:
N.75
Ligands:
ANP.4
No protein-ligand interaction detected (PLIP)
MG.2:
2 residues within 4Å:
Chain B:
N.75
Ligands:
ANP.5
No protein-ligand interaction detected (PLIP)
1 x
CDX
:
(S)-4,4'-(1-METHYL-1,2-ETHANEDIYL)BIS-2,6-PIPERAZINEDIONE
(Non-covalent)
CDX.3:
14 residues within 4Å:
Chain A:
H.25
,
T.32
,
Y.33
,
N.147
,
Y.149
,
L.153
,
Q.370
Chain B:
H.25
,
T.32
,
Y.33
,
N.147
,
Y.149
,
L.153
,
Q.370
5
PLIP interactions
:
4 interactions with chain A
,
1 interactions with chain B
Hydrogen bonds:
A:T.32
,
A:Q.370
,
B:Q.370
Water bridges:
A:Q.22
,
A:Y.33
2 x
ANP
:
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
(Non-covalent)
ANP.4:
25 residues within 4Å:
Chain A:
E.71
,
N.75
,
N.79
,
R.82
,
N.104
,
I.109
,
I.125
,
F.126
,
T.131
,
S.132
,
S.133
,
N.134
,
G.145
,
R.146
,
N.147
,
G.148
,
Y.149
,
G.150
,
A.151
,
K.152
,
T.200
,
Q.370
,
K.372
Chain B:
Y.17
Ligands:
MG.1
24
PLIP interactions
:
23 interactions with chain A
,
1 interactions with chain B
Hydrogen bonds:
A:E.71
,
A:N.75
,
A:N.104
,
A:S.132
,
A:S.133
,
A:S.133
,
A:R.146
,
A:N.147
,
A:N.147
,
A:G.148
,
A:Y.149
,
A:G.150
,
A:A.151
,
A:Q.370
,
A:K.372
,
A:K.372
Water bridges:
A:E.71
,
A:D.78
,
A:N.104
,
A:N.104
,
A:N.104
,
A:S.133
,
B:Y.17
Salt bridges:
A:K.152
ANP.5:
25 residues within 4Å:
Chain A:
Y.17
Chain B:
E.71
,
N.75
,
N.79
,
R.82
,
N.104
,
I.109
,
I.125
,
F.126
,
T.131
,
S.132
,
S.133
,
N.134
,
G.145
,
R.146
,
N.147
,
G.148
,
Y.149
,
G.150
,
A.151
,
K.152
,
T.200
,
Q.370
,
K.372
Ligands:
MG.2
21
PLIP interactions
:
21 interactions with chain B
Hydrogen bonds:
B:N.75
,
B:N.104
,
B:S.132
,
B:S.133
,
B:S.133
,
B:N.134
,
B:R.146
,
B:N.147
,
B:G.148
,
B:Y.149
,
B:Y.149
,
B:G.150
,
B:A.151
,
B:Q.370
,
B:K.372
,
B:K.372
Water bridges:
B:D.78
,
B:N.104
,
B:N.104
,
B:N.104
Salt bridges:
B:K.152
Links
RCSB
PDBe
PDBe-KB
PDBj
PDBsum
CATH
PLIP
Citation
Classen, S. et al., Structure of the topoisomerase II ATPase region and its mechanism of inhibition by the chemotherapeutic agent ICRF-187. Proc.Natl.Acad.Sci.USA (2003)
Release Date
2003-09-30
Peptides
DNA topoisomerase II:
A
B
SMTL:PDB
SMTL Chain Id:
PDB Chain Id:
A
A
B
B
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DNA topoisomerase II
Related Entries With Identical Sequence
1pvg.1
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