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5CDO
Asym. Unit
Info
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
(8, 25)
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)
View:
Select:
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
2
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
5
Ligand/Ion
GLYCEROL
5
MN
4
Ligand/Ion
MANGANESE (II) ION
6
NA
5
Ligand/Ion
SODIUM ION
7
PTR
4
Mod. Amino Acid
O-PHOSPHOTYROSINE
8
SO4
3
Ligand/Ion
SULFATE ION
[
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]
Sites
(21, 21)
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)
15: AD6 (SOFTWARE)
16: AD7 (SOFTWARE)
17: AD8 (SOFTWARE)
18: AD9 (SOFTWARE)
19: AE1 (SOFTWARE)
20: AE2 (SOFTWARE)
21: AE3 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
ARG A:429 , ARG C:429
binding site for residue SO4 A 501
02
AC2
SOFTWARE
TYR A:322 , LYS A:323 , THR A:325 , GLN A:328
binding site for residue NA A 502
03
AC3
SOFTWARE
ARG A:47 , ARG A:48 , GLU A:156 , PRO A:157
binding site for residue GOL A 503
04
AC4
SOFTWARE
ASP B:508 , ASP B:510 , HOH B:801 , HOH B:802 , HOH B:805 , HOH E:2202
binding site for residue MN B 701
05
AC5
SOFTWARE
GLY C:152 , ASN C:153 , GLU C:154
binding site for residue NA C 501
06
AC6
SOFTWARE
TYR C:322 , LYS C:323 , THR C:325 , GLN C:328
binding site for residue NA C 502
07
AC7
SOFTWARE
ASP D:508 , ASP D:510 , HOH D:1101 , HOH D:1102 , HOH D:1103 , HOH D:1104
binding site for residue MN D 1001
08
AC8
SOFTWARE
ASN D:474 , ASN D:475 , ASN D:476 , DG E:2013
binding site for residue GOL D 1002
09
AC9
SOFTWARE
SER A:297 , SER D:445 , GLY D:446
binding site for residue GOL D 1003
10
AD1
SOFTWARE
GLY B:436 , ASP B:437 , ARG B:458 , PTR C:123 , DC E:8 , DG E:2009 , DC F:2012 , DG F:2013
binding site for residue 53M E 2101
11
AD2
SOFTWARE
PTR A:123 , GLY D:436 , ASP D:437 , ARG D:458 , GLY D:459 , DC E:2012 , DG E:2013 , DC F:8 , DG F:2009 , HOH F:2202
binding site for residue 53L F 2101
12
AD3
SOFTWARE
TYR R:322 , THR R:325 , GLN R:328
binding site for residue NA R 501
13
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
14
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
15
AD6
SOFTWARE
ARG R:429 , ARG T:429 , ARG T:432
binding site for residue SO4 T 501
16
AD7
SOFTWARE
PRO T:44 , ARG T:47 , GLU T:156 , PRO T:157 , SER T:158
binding site for residue SO4 T 502
17
AD8
SOFTWARE
TYR T:322 , THR T:325 , GLN T:328 , HOH T:615
binding site for residue NA T 503
18
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
19
AE1
SOFTWARE
ASN U:476 , DG W:2013
binding site for residue GOL U 5002
20
AE2
SOFTWARE
GLY U:446 , ARG U:447 , TRP U:592
binding site for residue GOL U 5003
21
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)
Info
(mutated residues are not available)
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PROSITE Patterns/Profiles
(0, 0)
Info
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;
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Exons
(0, 0)
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Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
SCOP Domains
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CATH Domains
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Pfam Domains
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Show PDB file:
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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