Summary Structural details Experimental details Functional details Sequence Neighbor History Downloads

4DYU

The crystal structure of DNA starvation/stationary phase protection protein Dps from Yersinia pestis KIM 10

Functional Information from GO Data

Chain	GOid	namespace	contents
A	0003677	molecular_function	DNA binding
A	0005737	cellular_component	cytoplasm
A	0008199	molecular_function	ferric iron binding
A	0016491	molecular_function	oxidoreductase activity
A	0016722	molecular_function	oxidoreductase activity, acting on metal ions
A	0030261	biological_process	chromosome condensation
A	0032297	biological_process	negative regulation of DNA-templated DNA replication initiation
A	0046872	molecular_function	metal ion binding
A	1990084	cellular_component	DnaA-Dps complex
B	0003677	molecular_function	DNA binding
B	0005737	cellular_component	cytoplasm
B	0008199	molecular_function	ferric iron binding
B	0016491	molecular_function	oxidoreductase activity
B	0016722	molecular_function	oxidoreductase activity, acting on metal ions
B	0030261	biological_process	chromosome condensation
B	0032297	biological_process	negative regulation of DNA-templated DNA replication initiation
B	0046872	molecular_function	metal ion binding
B	1990084	cellular_component	DnaA-Dps complex
C	0003677	molecular_function	DNA binding
C	0005737	cellular_component	cytoplasm
C	0008199	molecular_function	ferric iron binding
C	0016491	molecular_function	oxidoreductase activity
C	0016722	molecular_function	oxidoreductase activity, acting on metal ions
C	0030261	biological_process	chromosome condensation
C	0032297	biological_process	negative regulation of DNA-templated DNA replication initiation
C	0046872	molecular_function	metal ion binding
C	1990084	cellular_component	DnaA-Dps complex
D	0003677	molecular_function	DNA binding
D	0005737	cellular_component	cytoplasm
D	0008199	molecular_function	ferric iron binding
D	0016491	molecular_function	oxidoreductase activity
D	0016722	molecular_function	oxidoreductase activity, acting on metal ions
D	0030261	biological_process	chromosome condensation
D	0032297	biological_process	negative regulation of DNA-templated DNA replication initiation
D	0046872	molecular_function	metal ion binding
D	1990084	cellular_component	DnaA-Dps complex
E	0003677	molecular_function	DNA binding
E	0005737	cellular_component	cytoplasm
E	0008199	molecular_function	ferric iron binding
E	0016491	molecular_function	oxidoreductase activity
E	0016722	molecular_function	oxidoreductase activity, acting on metal ions
E	0030261	biological_process	chromosome condensation
E	0032297	biological_process	negative regulation of DNA-templated DNA replication initiation
E	0046872	molecular_function	metal ion binding
E	1990084	cellular_component	DnaA-Dps complex
F	0003677	molecular_function	DNA binding
F	0005737	cellular_component	cytoplasm
F	0008199	molecular_function	ferric iron binding
F	0016491	molecular_function	oxidoreductase activity
F	0016722	molecular_function	oxidoreductase activity, acting on metal ions
F	0030261	biological_process	chromosome condensation
F	0032297	biological_process	negative regulation of DNA-templated DNA replication initiation
F	0046872	molecular_function	metal ion binding
F	1990084	cellular_component	DnaA-Dps complex
G	0003677	molecular_function	DNA binding
G	0005737	cellular_component	cytoplasm
G	0008199	molecular_function	ferric iron binding
G	0016491	molecular_function	oxidoreductase activity
G	0016722	molecular_function	oxidoreductase activity, acting on metal ions
G	0030261	biological_process	chromosome condensation
G	0032297	biological_process	negative regulation of DNA-templated DNA replication initiation
G	0046872	molecular_function	metal ion binding
G	1990084	cellular_component	DnaA-Dps complex
H	0003677	molecular_function	DNA binding
H	0005737	cellular_component	cytoplasm
H	0008199	molecular_function	ferric iron binding
H	0016491	molecular_function	oxidoreductase activity
H	0016722	molecular_function	oxidoreductase activity, acting on metal ions
H	0030261	biological_process	chromosome condensation
H	0032297	biological_process	negative regulation of DNA-templated DNA replication initiation
H	0046872	molecular_function	metal ion binding
H	1990084	cellular_component	DnaA-Dps complex
I	0003677	molecular_function	DNA binding
I	0005737	cellular_component	cytoplasm
I	0008199	molecular_function	ferric iron binding
I	0016491	molecular_function	oxidoreductase activity
I	0016722	molecular_function	oxidoreductase activity, acting on metal ions
I	0030261	biological_process	chromosome condensation
I	0032297	biological_process	negative regulation of DNA-templated DNA replication initiation
I	0046872	molecular_function	metal ion binding
I	1990084	cellular_component	DnaA-Dps complex
J	0003677	molecular_function	DNA binding
J	0005737	cellular_component	cytoplasm
J	0008199	molecular_function	ferric iron binding
J	0016491	molecular_function	oxidoreductase activity
J	0016722	molecular_function	oxidoreductase activity, acting on metal ions
J	0030261	biological_process	chromosome condensation
J	0032297	biological_process	negative regulation of DNA-templated DNA replication initiation
J	0046872	molecular_function	metal ion binding
J	1990084	cellular_component	DnaA-Dps complex
K	0003677	molecular_function	DNA binding
K	0005737	cellular_component	cytoplasm
K	0008199	molecular_function	ferric iron binding
K	0016491	molecular_function	oxidoreductase activity
K	0016722	molecular_function	oxidoreductase activity, acting on metal ions
K	0030261	biological_process	chromosome condensation
K	0032297	biological_process	negative regulation of DNA-templated DNA replication initiation
K	0046872	molecular_function	metal ion binding
K	1990084	cellular_component	DnaA-Dps complex
L	0003677	molecular_function	DNA binding
L	0005737	cellular_component	cytoplasm
L	0008199	molecular_function	ferric iron binding
L	0016491	molecular_function	oxidoreductase activity
L	0016722	molecular_function	oxidoreductase activity, acting on metal ions
L	0030261	biological_process	chromosome condensation
L	0032297	biological_process	negative regulation of DNA-templated DNA replication initiation
L	0046872	molecular_function	metal ion binding
L	1990084	cellular_component	DnaA-Dps complex

Functional Information from PDB Data

site_id	AC1
Number of Residues	3
Details	BINDING SITE FOR RESIDUE ZN A 201

Chain	Residue
A	ASP78
A	GLU82
C	HIS51

site_id	AC2
Number of Residues	4
Details	BINDING SITE FOR RESIDUE SO4 A 202

Chain	Residue
A	ARG70
A	THR74
C	ARG70
C	THR74

site_id	AC3
Number of Residues	6
Details	BINDING SITE FOR RESIDUE SO4 A 203

Chain	Residue
A	GLU167
H	ALA57
K	ALA57
K	ASN58
A	ALA57
A	ASN58

site_id	AC4
Number of Residues	4
Details	BINDING SITE FOR RESIDUE ZN B 201

Chain	Residue
B	ASP78
B	GLU82
D	HIS51
D	ASP67

site_id	AC5
Number of Residues	4
Details	BINDING SITE FOR RESIDUE SO4 B 202

Chain	Residue
B	ARG70
B	THR74
D	ARG70
D	THR74

site_id	AC6
Number of Residues	8
Details	BINDING SITE FOR RESIDUE SO4 B 203

Chain	Residue
B	ALA57
B	ASN58
F	ALA57
F	ASN58
F	GLU167
J	ALA57
J	GLU167
J	HOH301

site_id	AC7
Number of Residues	4
Details	BINDING SITE FOR RESIDUE ZN C 201

Chain	Residue
A	HIS51
A	ASP67
C	ASP78
C	GLU82

site_id	AC8
Number of Residues	3
Details	BINDING SITE FOR RESIDUE ZN D 201

Chain	Residue
B	HIS51
D	ASP78
D	GLU82

site_id	AC9
Number of Residues	8
Details	BINDING SITE FOR RESIDUE SO4 D 202

Chain	Residue
D	ALA57
D	ASN58
D	GLU167
G	ALA57
G	GLU167
I	ALA57
I	GLU167
I	HOH301

site_id	BC1
Number of Residues	2
Details	BINDING SITE FOR RESIDUE SO4 D 203

Chain	Residue
D	LYS105
D	ARG124

site_id	BC2
Number of Residues	4
Details	BINDING SITE FOR RESIDUE ZN E 201

Chain	Residue
E	ASP78
E	GLU82
G	HIS51
G	ASP67

site_id	BC3
Number of Residues	5
Details	BINDING SITE FOR RESIDUE ZN E 202

Chain	Residue
E	HIS51
E	HOH311
G	ASP78
G	GLU82
G	HOH312

site_id	BC4
Number of Residues	4
Details	BINDING SITE FOR RESIDUE SO4 E 203

Chain	Residue
E	ARG70
E	THR74
G	ARG70
G	THR74

site_id	BC5
Number of Residues	3
Details	BINDING SITE FOR RESIDUE ZN F 201

Chain	Residue
F	ASP78
F	GLU82
H	HIS51

site_id	BC6
Number of Residues	2
Details	BINDING SITE FOR RESIDUE SO4 F 202

Chain	Residue
F	LYS105
F	SER106

site_id	BC7
Number of Residues	4
Details	BINDING SITE FOR RESIDUE SO4 G 201

Chain	Residue
G	LYS105
G	SER106
I	LYS105
I	SER106

site_id	BC8
Number of Residues	4
Details	BINDING SITE FOR RESIDUE ZN H 201

Chain	Residue
F	LYS48
F	HIS51
H	ASP78
H	GLU82

site_id	BC9
Number of Residues	4
Details	BINDING SITE FOR RESIDUE SO4 H 202

Chain	Residue
F	ARG70
F	THR74
H	ARG70
H	THR74

site_id	CC1
Number of Residues	3
Details	BINDING SITE FOR RESIDUE ZN I 201

Chain	Residue
I	ASP78
I	GLU82
K	HIS51

site_id	CC2
Number of Residues	4
Details	BINDING SITE FOR RESIDUE ZN J 201

Chain	Residue
J	ASP78
J	GLU82
L	HIS51
L	ASP67

site_id	CC3
Number of Residues	4
Details	BINDING SITE FOR RESIDUE SO4 J 202

Chain	Residue
J	ARG70
J	THR74
J	HOH303
L	THR74

site_id	CC4
Number of Residues	6
Details	BINDING SITE FOR RESIDUE SO4 J 203

Chain	Residue
B	LYS105
B	SER106
J	LYS105
J	SER106
J	HOH304
J	HOH312

site_id	CC5
Number of Residues	3
Details	BINDING SITE FOR RESIDUE ZN K 201

Chain	Residue
I	HIS51
K	ASP78
K	GLU82

site_id	CC6
Number of Residues	4
Details	BINDING SITE FOR RESIDUE SO4 K 202

Chain	Residue
K	THR74
I	ARG70
I	THR74
K	ARG70

site_id	CC7
Number of Residues	3
Details	BINDING SITE FOR RESIDUE ZN L 201

Chain	Residue
J	HIS51
L	ASP78
L	GLU82

Functional Information from PROSITE/UniProt

site_id	PS00818
Number of Residues	17
Details	DPS_1 Dps protein family signature 1. HWnMrGanfvaVHemlD

Chain	Residue	Details
A	HIS51-ASP67

Functional Information from SwissProt/UniProt

site_id	SWS_FT_FI1
Number of Residues	36
Details	Binding site: {"evidences":[{"source":"HAMAP-Rule","id":"MF_01441","evidenceCode":"ECO:0000255"}]}

Chain

Residue

Details

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