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5CDN
Asym. Unit
Info
Asym.Unit (983 KB)
Biol.Unit 1 (489 KB)
Biol.Unit 2 (487 KB)
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(1)
Title
:
2.8A STRUCTURE OF ETOPOSIDE WITH S.AUREUS DNA GYRASE AND DNA
Authors
:
B. D. Bax, V. Srikannathasan, P. F. Chan
Date
:
04 Jul 15 (Deposition) - 16 Dec 15 (Release) - 16 Dec 15 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.79
Chains
:
Asym. Unit : A,B,C,D,E,F,G,N,O,P,R,S,T,U,V,W
Biol. Unit 1: A,B,C,D,E,F,G,O (1x)
Biol. Unit 2: N,P,R,S,T,U,V,W (1x)
Keywords
:
Type Iia Topoisomerase, Antibacterial, Inhibitor, Isomerase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
P. F. Chan, V. Srikannathasan, J. Huang, H. Cui, A. P. Fosberry, M. Gu, M. M. Hann, M. Hibbs, P. Homes, K. Ingraham, J. Pizzollo, C. Shen, A. J. Shillings, C. E. Spitzfaden, R. Tanner, A. J. Theobald, R. A. Stavenger, B. D. Bax, M. N. Gwynn
Structural Basis Of Dna Gyrase Inhibition By Antibacterial Qpt-1, Anticancer Drug Etoposide And Moxifloxacin.
Nat Commun V. 6 10048 2015
(for further references see the
PDB file header
)
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Hetero Components
(6, 18)
Info
All Hetero Components
1a: (5S,5AR,8AR,9R)-9-(4-HYDROXY-3,5-D... (EVPa)
1b: (5S,5AR,8AR,9R)-9-(4-HYDROXY-3,5-D... (EVPb)
1c: (5S,5AR,8AR,9R)-9-(4-HYDROXY-3,5-D... (EVPc)
1d: (5S,5AR,8AR,9R)-9-(4-HYDROXY-3,5-D... (EVPd)
2a: GLYCEROL (GOLa)
2b: GLYCEROL (GOLb)
2c: GLYCEROL (GOLc)
2d: GLYCEROL (GOLd)
3a: MANGANESE (II) ION (MNa)
3b: MANGANESE (II) ION (MNb)
3c: MANGANESE (II) ION (MNc)
3d: MANGANESE (II) ION (MNd)
4a: SODIUM ION (NAa)
5a: O-PHOSPHOTYROSINE (PTRa)
5b: O-PHOSPHOTYROSINE (PTRb)
5c: O-PHOSPHOTYROSINE (PTRc)
5d: O-PHOSPHOTYROSINE (PTRd)
6a: SULFATE ION (SO4a)
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No.
Name
Count
Type
Full Name
1
EVP
4
Ligand/Ion
(5S,5AR,8AR,9R)-9-(4-HYDROXY-3,5-DIMETHOXYPHENYL)-8-OXO-5,5A,6,8,8A,9-HEXAHYDROFURO[3',4':6,7]NAPHTHO[2,3-D][1,3]DIOXOL-5-YL 4,6-O-[(1R)-ETHYLIDENE]-BETA-D-GLUCOPYRANOSIDE
2
GOL
4
Ligand/Ion
GLYCEROL
3
MN
4
Ligand/Ion
MANGANESE (II) ION
4
NA
1
Ligand/Ion
SODIUM ION
5
PTR
4
Mod. Amino Acid
O-PHOSPHOTYROSINE
6
SO4
1
Ligand/Ion
SULFATE ION
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Sites
(14, 14)
Info
All Sites
01: AC1 (SOFTWARE)
02: AC2 (SOFTWARE)
03: AC3 (SOFTWARE)
04: AC4 (SOFTWARE)
05: AC5 (SOFTWARE)
06: AC6 (SOFTWARE)
07: AC7 (SOFTWARE)
08: AC8 (SOFTWARE)
09: AC9 (SOFTWARE)
10: AD1 (SOFTWARE)
11: AD2 (SOFTWARE)
12: AD3 (SOFTWARE)
13: AD4 (SOFTWARE)
14: AD5 (SOFTWARE)
View:
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No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
PRO A:44 , ARG A:47 , ARG A:48 , ILE A:147 , GLU A:156 , SER A:158
binding site for residue SO4 A 501
02
AC2
SOFTWARE
GLU B:435 , ASP B:508 , ASP B:510 , HOH B:1102 , HOH B:1106 , HOH B:1109 , HOH B:1123
binding site for residue MN B 1001
03
AC3
SOFTWARE
MET C:113 , GLY C:115 , VAL C:268 , ASN C:269
binding site for residue GOL C 501
04
AC4
SOFTWARE
TYR C:322 , LYS C:323 , THR C:325 , GLN C:328
binding site for residue NA C 502
05
AC5
SOFTWARE
ARG C:377 , ARG C:432
binding site for residue GOL C 503
06
AC6
SOFTWARE
GLU D:435 , ASP D:508 , ASP D:510 , HOH D:1103 , HOH D:1108 , HOH D:1111 , HOH E:204
binding site for residue MN D 1001
07
AC7
SOFTWARE
DC E:4 , DG E:5 , DT E:6 , DA E:7 , DT O:2014
binding site for residue GOL E 101
08
AC8
SOFTWARE
SER A:84 , GLU A:88 , GLY B:436 , ASP B:437 , ARG B:458 , GLY B:459 , DC F:8 , DC G:2012 , DG G:2013 , DG O:2009 , DG O:2010
binding site for residue EVP G 2101
09
AC9
SOFTWARE
PTR A:123 , SER C:84 , GLY D:436 , ASP D:437 , ARG D:458 , GLY D:459 , DC E:8 , DG G:2009 , DC O:2012 , DG O:2013
binding site for residue EVP O 2101
10
AD1
SOFTWARE
GLU S:435 , ASP S:508 , ASP S:510 , HOH S:6102 , HOH S:6108 , HOH W:102 , HOH W:106
binding site for residue MN S 6001
11
AD2
SOFTWARE
VAL T:31 , PRO T:44 , ARG T:47 , ILE T:147 , GLU T:156
binding site for residue GOL T 501
12
AD3
SOFTWARE
GLU U:435 , ASP U:508 , ASP U:510 , HOH U:1102 , HOH U:1105 , HOH V:102 , HOH V:104
binding site for residue MN U 1001
13
AD4
SOFTWARE
DC N:2012 , DG N:2013 , DG P:2009 , DG P:2010 , SER R:84 , GLU R:88 , GLY S:436 , ASP S:437 , ARG S:458 , GLY S:459 , DC W:8
binding site for residue EVP N 2101
14
AD5
SOFTWARE
DG N:2009 , DG N:2010 , DC P:2012 , DG P:2013 , PTR R:123 , SER T:84 , GLU T:88 , GLY U:436 , ASP U:437 , ARG U:458 , GLY U:459 , DC V:8
binding site for residue EVP P 2101
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SAPs(SNPs)/Variants
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Exons
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Asymmetric Unit 1
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Asym.Unit (983 KB)
Header - Asym.Unit
Biol.Unit 1 (489 KB)
Header - Biol.Unit 1
Biol.Unit 2 (487 KB)
Header - Biol.Unit 2
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