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5CDO
Biol. Unit 2
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Asym.Unit (1.4 MB)
Biol.Unit 1 (693 KB)
Biol.Unit 2 (684 KB)
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(1)
Title
:
3.15A STRUCTURE OF QPT-1 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
:
3.15
Chains
:
Asym. Unit : A,B,C,D,E,F,R,S,T,U,V,W
Biol. Unit 1: A,B,C,D,E,F (1x)
Biol. Unit 2: 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
(5, 8)
Info
All Hetero Components
1a: (2R,4S,4AS,5R)-6'-HYDROXY-2,4-DIME... (50Ma)
2a: (2R,4S,4AS,5S)-6'-HYDROXY-2,4-DIME... (53La)
3a: (2R,4S,4AS)-4',6'-DIHYDROXY-2,4-DI... (53Ma)
3b: (2R,4S,4AS)-4',6'-DIHYDROXY-2,4-DI... (53Mb)
4a: GLYCEROL (GOLa)
4b: GLYCEROL (GOLb)
4c: GLYCEROL (GOLc)
4d: GLYCEROL (GOLd)
4e: GLYCEROL (GOLe)
5a: MANGANESE (II) ION (MNa)
5b: MANGANESE (II) ION (MNb)
5c: MANGANESE (II) ION (MNc)
5d: MANGANESE (II) ION (MNd)
6a: SODIUM ION (NAa)
6b: SODIUM ION (NAb)
6c: SODIUM ION (NAc)
6d: SODIUM ION (NAd)
6e: SODIUM ION (NAe)
7a: O-PHOSPHOTYROSINE (PTRa)
7b: O-PHOSPHOTYROSINE (PTRb)
7c: O-PHOSPHOTYROSINE (PTRc)
7d: O-PHOSPHOTYROSINE (PTRd)
8a: SULFATE ION (SO4a)
8b: SULFATE ION (SO4b)
8c: SULFATE ION (SO4c)
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Label:
No.
Name
Count
Type
Full Name
1
50M
1
Ligand/Ion
(2R,4S,4AS,5R)-6'-HYDROXY-2,4-DIMETHYL-8-NITRO-1,2,4,4A-TETRAHYDRO-2'H,6H-SPIRO[1,4-OXAZINO[4,3-A]QUINOLINE-5,5'-PYRIMIDINE]-2',4'(3'H)-DIONE
2
53L
-1
Ligand/Ion
(2R,4S,4AS,5S)-6'-HYDROXY-2,4-DIMETHYL-8-NITRO-1,2,4,4A-TETRAHYDRO-2'H,6H-SPIRO[1,4-OXAZINO[4,3-A]QUINOLINE-5,5'-PYRIMIDINE]-2',4'(3'H)-DIONE
3
53M
1
Ligand/Ion
(2R,4S,4AS)-4',6'-DIHYDROXY-2,4-DIMETHYL-8-NITRO-1,2,4,4A-TETRAHYDRO-2'H,6H-SPIRO[1,4-OXAZINO[4,3-A]QUINOLINE-5,5'-PYRIMIDIN]-2'-ONE
4
GOL
2
Ligand/Ion
GLYCEROL
5
MN
-1
Ligand/Ion
MANGANESE (II) ION
6
NA
-1
Ligand/Ion
SODIUM ION
7
PTR
2
Mod. Amino Acid
O-PHOSPHOTYROSINE
8
SO4
2
Ligand/Ion
SULFATE ION
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Sites
(10, 10)
Info
All Sites
01: AD3 (SOFTWARE)
02: AD4 (SOFTWARE)
03: AD5 (SOFTWARE)
04: AD6 (SOFTWARE)
05: AD7 (SOFTWARE)
06: AD8 (SOFTWARE)
07: AD9 (SOFTWARE)
08: AE1 (SOFTWARE)
09: AE2 (SOFTWARE)
10: AE3 (SOFTWARE)
View:
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No.
Name
Evidence
Residues
Description
01
AD3
SOFTWARE
TYR R:322 , THR R:325 , GLN R:328
binding site for residue NA R 501
02
AD4
SOFTWARE
ASP S:508 , ASP S:510 , HOH S:6103 , HOH S:6104 , HOH S:6106 , HOH S:6107
binding site for residue MN S 6001
03
AD5
SOFTWARE
GLY S:436 , ASP S:437 , ARG S:458 , GLY S:459 , HOH S:6102 , PTR T:123 , DC V:2012 , DG V:2013 , DC W:8 , DG W:2009
binding site for residue 50M S 6002
04
AD6
SOFTWARE
ARG R:429 , ARG T:429 , ARG T:432
binding site for residue SO4 T 501
05
AD7
SOFTWARE
PRO T:44 , ARG T:47 , GLU T:156 , PRO T:157 , SER T:158
binding site for residue SO4 T 502
06
AD8
SOFTWARE
TYR T:322 , THR T:325 , GLN T:328 , HOH T:615
binding site for residue NA T 503
07
AD9
SOFTWARE
ASP U:508 , ASP U:510 , HOH U:5101 , HOH U:5102 , HOH U:5107 , HOH V:2102
binding site for residue MN U 5001
08
AE1
SOFTWARE
ASN U:476 , DG W:2013
binding site for residue GOL U 5002
09
AE2
SOFTWARE
GLY U:446 , ARG U:447 , TRP U:592
binding site for residue GOL U 5003
10
AE3
SOFTWARE
GLY U:436 , ASP U:437 , ARG U:458 , GLY U:459 , DC V:8 , DG V:2009 , DC W:2012 , DG W:2013
binding site for residue 53M W 2101
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SAPs(SNPs)/Variants
(0, 0)
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Exons
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Asymmetric Unit 1
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Asym.Unit (1.4 MB)
Header - Asym.Unit
Biol.Unit 1 (693 KB)
Header - Biol.Unit 1
Biol.Unit 2 (684 KB)
Header - Biol.Unit 2
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