Summary Structural details Experimental details Functional details Sequence Neighbor History Downloads

5CDO

3.15A structure of QPT-1 with S.aureus DNA gyrase and DNA

Functional Information from GO Data

Chain	GOid	namespace	contents
A	0003677	molecular_function	DNA binding
A	0003918	molecular_function	DNA topoisomerase type II (double strand cut, ATP-hydrolyzing) activity
A	0005524	molecular_function	ATP binding
A	0006259	biological_process	DNA metabolic process
A	0006265	biological_process	DNA topological change
B	0003677	molecular_function	DNA binding
B	0003918	molecular_function	DNA topoisomerase type II (double strand cut, ATP-hydrolyzing) activity
B	0005524	molecular_function	ATP binding
B	0006265	biological_process	DNA topological change
C	0003677	molecular_function	DNA binding
C	0003918	molecular_function	DNA topoisomerase type II (double strand cut, ATP-hydrolyzing) activity
C	0005524	molecular_function	ATP binding
C	0006259	biological_process	DNA metabolic process
C	0006265	biological_process	DNA topological change
D	0003677	molecular_function	DNA binding
D	0003918	molecular_function	DNA topoisomerase type II (double strand cut, ATP-hydrolyzing) activity
D	0005524	molecular_function	ATP binding
D	0006265	biological_process	DNA topological change
R	0003677	molecular_function	DNA binding
R	0003918	molecular_function	DNA topoisomerase type II (double strand cut, ATP-hydrolyzing) activity
R	0005524	molecular_function	ATP binding
R	0006259	biological_process	DNA metabolic process
R	0006265	biological_process	DNA topological change
S	0003677	molecular_function	DNA binding
S	0003918	molecular_function	DNA topoisomerase type II (double strand cut, ATP-hydrolyzing) activity
S	0005524	molecular_function	ATP binding
S	0006265	biological_process	DNA topological change
T	0003677	molecular_function	DNA binding
T	0003918	molecular_function	DNA topoisomerase type II (double strand cut, ATP-hydrolyzing) activity
T	0005524	molecular_function	ATP binding
T	0006259	biological_process	DNA metabolic process
T	0006265	biological_process	DNA topological change
U	0003677	molecular_function	DNA binding
U	0003918	molecular_function	DNA topoisomerase type II (double strand cut, ATP-hydrolyzing) activity
U	0005524	molecular_function	ATP binding
U	0006265	biological_process	DNA topological change

Functional Information from PDB Data

site_id	AC1
Number of Residues	2
Details	binding site for residue SO4 A 501

Chain	Residue
A	ARG429
C	ARG429

site_id	AC2
Number of Residues	4
Details	binding site for residue NA A 502

Chain	Residue
A	TYR322
A	LYS323
A	THR325
A	GLN328

site_id	AC3
Number of Residues	4
Details	binding site for residue GOL A 503

Chain	Residue
A	PRO157
A	ARG47
A	ARG48
A	GLU156

site_id	AC4
Number of Residues	6
Details	binding site for residue MN B 701

Chain	Residue
B	ASP508
B	ASP510
B	HOH801
B	HOH802
B	HOH805
E	HOH2202

site_id	AC5
Number of Residues	3
Details	binding site for residue NA C 501

Chain	Residue
C	GLY152
C	ASN153
C	GLU154

site_id	AC6
Number of Residues	4
Details	binding site for residue NA C 502

Chain	Residue
C	TYR322
C	LYS323
C	THR325
C	GLN328

site_id	AC7
Number of Residues	6
Details	binding site for residue MN D 1001

Chain	Residue
D	ASP508
D	ASP510
D	HOH1101
D	HOH1102
D	HOH1103
D	HOH1104

site_id	AC8
Number of Residues	4
Details	binding site for residue GOL D 1002

Chain	Residue
D	ASN474
D	ASN475
D	ASN476
E	DG2013

site_id	AC9
Number of Residues	3
Details	binding site for residue GOL D 1003

Chain	Residue
A	SER297
D	SER445
D	GLY446

site_id	AD1
Number of Residues	8
Details	binding site for residue 53M E 2101

Chain	Residue
B	GLY436
B	ASP437
B	ARG458
C	PTR123
E	DC8
E	DG2009
F	DC2012
F	DG2013

site_id	AD2
Number of Residues	10
Details	binding site for residue 53L F 2101

Chain	Residue
A	PTR123
D	GLY436
D	ASP437
D	ARG458
D	GLY459
E	DC2012
E	DG2013
F	DC8
F	DG2009
F	HOH2202

site_id	AD3
Number of Residues	3
Details	binding site for residue NA R 501

Chain	Residue
R	TYR322
R	THR325
R	GLN328

site_id	AD4
Number of Residues	6
Details	binding site for residue MN S 6001

Chain	Residue
S	ASP508
S	ASP510
S	HOH6103
S	HOH6104
S	HOH6106
S	HOH6107

site_id	AD5
Number of Residues	10
Details	binding site for residue 50M S 6002

Chain	Residue
S	GLY436
S	ASP437
S	ARG458
S	GLY459
S	HOH6102
T	PTR123
V	DC2012
V	DG2013
W	DC8
W	DG2009

site_id	AD6
Number of Residues	3
Details	binding site for residue SO4 T 501

Chain	Residue
R	ARG429
T	ARG429
T	ARG432

site_id	AD7
Number of Residues	5
Details	binding site for residue SO4 T 502

Chain	Residue
T	PRO44
T	ARG47
T	GLU156
T	PRO157
T	SER158

site_id	AD8
Number of Residues	4
Details	binding site for residue NA T 503

Chain	Residue
T	TYR322
T	THR325
T	GLN328
T	HOH615

site_id	AD9
Number of Residues	6
Details	binding site for residue MN U 5001

Chain	Residue
U	ASP508
U	ASP510
U	HOH5101
U	HOH5102
U	HOH5107
V	HOH2102

site_id	AE1
Number of Residues	2
Details	binding site for residue GOL U 5002

Chain	Residue
U	ASN476
W	DG2013

site_id	AE2
Number of Residues	3
Details	binding site for residue GOL U 5003

Chain	Residue
U	GLY446
U	ARG447
U	TRP592

site_id	AE3
Number of Residues	8
Details	binding site for residue 53M W 2101

Chain	Residue
U	GLY459
V	DC8
V	DG2009
W	DC2012
W	DG2013
U	GLY436
U	ASP437
U	ARG458

Functional Information from PROSITE/UniProt

site_id	PS00177
Number of Residues	9
Details	TOPOISOMERASE_II DNA topoisomerase II signature. LVEGDSAGG

Chain	Residue	Details
B	LEU433-GLY441

Functional Information from SwissProt/UniProt

site_id	SWS_FT_FI1
Number of Residues	4
Details	Active site: {"description":"O-(5'-phospho-DNA)-tyrosine intermediate","evidences":[{"source":"HAMAP-Rule","id":"MF_01897","evidenceCode":"ECO:0000255"}]}

Chain

Residue

Details

site_id	SWS_FT_FI2
Number of Residues	456
Details	Domain: {"description":"Toprim","evidences":[{"source":"HAMAP-Rule","id":"MF_01898","evidenceCode":"ECO:0000255"}]}

Chain

Residue

Details

site_id	SWS_FT_FI3
Number of Residues	12
Details	Binding site: {"evidences":[{"source":"HAMAP-Rule","id":"MF_01898","evidenceCode":"ECO:0000255"}]}

Chain

Residue

Details

site_id	SWS_FT_FI4
Number of Residues	8
Details	Site: {"description":"Interaction with DNA","evidences":[{"source":"HAMAP-Rule","id":"MF_01898","evidenceCode":"ECO:0000255"}]}

Chain

Residue

Details

		Sequence (fasta)
		PDBx/mmCIF
		PDBML format (no-atom)
		PDB format (full)
		Validation report (PDF)
		EDMap 2fo-fc (MTZ)