Summary Structural details Experimental details Functional details Sequence Neighbor History Downloads

5CB5

Structural Insights into the Mechanism of Escherichia coli Ymdb

Functional Information from GO Data

Chain	GOid	namespace	contents
A	0001883	molecular_function	purine nucleoside binding
A	0008428	molecular_function	ribonuclease inhibitor activity
A	0016787	molecular_function	hydrolase activity
A	0019213	molecular_function	deacetylase activity
A	0019899	molecular_function	enzyme binding
A	0042278	biological_process	purine nucleoside metabolic process
A	0046677	biological_process	response to antibiotic
A	0060698	molecular_function	endoribonuclease inhibitor activity
A	0061463	molecular_function	O-acetyl-ADP-ribose deacetylase activity
A	1900231	biological_process	regulation of single-species biofilm formation on inanimate substrate
B	0001883	molecular_function	purine nucleoside binding
B	0008428	molecular_function	ribonuclease inhibitor activity
B	0016787	molecular_function	hydrolase activity
B	0019213	molecular_function	deacetylase activity
B	0019899	molecular_function	enzyme binding
B	0042278	biological_process	purine nucleoside metabolic process
B	0046677	biological_process	response to antibiotic
B	0060698	molecular_function	endoribonuclease inhibitor activity
B	0061463	molecular_function	O-acetyl-ADP-ribose deacetylase activity
B	1900231	biological_process	regulation of single-species biofilm formation on inanimate substrate
C	0001883	molecular_function	purine nucleoside binding
C	0008428	molecular_function	ribonuclease inhibitor activity
C	0016787	molecular_function	hydrolase activity
C	0019213	molecular_function	deacetylase activity
C	0019899	molecular_function	enzyme binding
C	0042278	biological_process	purine nucleoside metabolic process
C	0046677	biological_process	response to antibiotic
C	0060698	molecular_function	endoribonuclease inhibitor activity
C	0061463	molecular_function	O-acetyl-ADP-ribose deacetylase activity
C	1900231	biological_process	regulation of single-species biofilm formation on inanimate substrate
D	0001883	molecular_function	purine nucleoside binding
D	0008428	molecular_function	ribonuclease inhibitor activity
D	0016787	molecular_function	hydrolase activity
D	0019213	molecular_function	deacetylase activity
D	0019899	molecular_function	enzyme binding
D	0042278	biological_process	purine nucleoside metabolic process
D	0046677	biological_process	response to antibiotic
D	0060698	molecular_function	endoribonuclease inhibitor activity
D	0061463	molecular_function	O-acetyl-ADP-ribose deacetylase activity
D	1900231	biological_process	regulation of single-species biofilm formation on inanimate substrate
E	0001883	molecular_function	purine nucleoside binding
E	0008428	molecular_function	ribonuclease inhibitor activity
E	0016787	molecular_function	hydrolase activity
E	0019213	molecular_function	deacetylase activity
E	0019899	molecular_function	enzyme binding
E	0042278	biological_process	purine nucleoside metabolic process
E	0046677	biological_process	response to antibiotic
E	0060698	molecular_function	endoribonuclease inhibitor activity
E	0061463	molecular_function	O-acetyl-ADP-ribose deacetylase activity
E	1900231	biological_process	regulation of single-species biofilm formation on inanimate substrate
F	0001883	molecular_function	purine nucleoside binding
F	0008428	molecular_function	ribonuclease inhibitor activity
F	0016787	molecular_function	hydrolase activity
F	0019213	molecular_function	deacetylase activity
F	0019899	molecular_function	enzyme binding
F	0042278	biological_process	purine nucleoside metabolic process
F	0046677	biological_process	response to antibiotic
F	0060698	molecular_function	endoribonuclease inhibitor activity
F	0061463	molecular_function	O-acetyl-ADP-ribose deacetylase activity
F	1900231	biological_process	regulation of single-species biofilm formation on inanimate substrate
G	0001883	molecular_function	purine nucleoside binding
G	0008428	molecular_function	ribonuclease inhibitor activity
G	0016787	molecular_function	hydrolase activity
G	0019213	molecular_function	deacetylase activity
G	0019899	molecular_function	enzyme binding
G	0042278	biological_process	purine nucleoside metabolic process
G	0046677	biological_process	response to antibiotic
G	0060698	molecular_function	endoribonuclease inhibitor activity
G	0061463	molecular_function	O-acetyl-ADP-ribose deacetylase activity
G	1900231	biological_process	regulation of single-species biofilm formation on inanimate substrate
H	0001883	molecular_function	purine nucleoside binding
H	0008428	molecular_function	ribonuclease inhibitor activity
H	0016787	molecular_function	hydrolase activity
H	0019213	molecular_function	deacetylase activity
H	0019899	molecular_function	enzyme binding
H	0042278	biological_process	purine nucleoside metabolic process
H	0046677	biological_process	response to antibiotic
H	0060698	molecular_function	endoribonuclease inhibitor activity
H	0061463	molecular_function	O-acetyl-ADP-ribose deacetylase activity
H	1900231	biological_process	regulation of single-species biofilm formation on inanimate substrate
I	0001883	molecular_function	purine nucleoside binding
I	0008428	molecular_function	ribonuclease inhibitor activity
I	0016787	molecular_function	hydrolase activity
I	0019213	molecular_function	deacetylase activity
I	0019899	molecular_function	enzyme binding
I	0042278	biological_process	purine nucleoside metabolic process
I	0046677	biological_process	response to antibiotic
I	0060698	molecular_function	endoribonuclease inhibitor activity
I	0061463	molecular_function	O-acetyl-ADP-ribose deacetylase activity
I	1900231	biological_process	regulation of single-species biofilm formation on inanimate substrate
J	0001883	molecular_function	purine nucleoside binding
J	0008428	molecular_function	ribonuclease inhibitor activity
J	0016787	molecular_function	hydrolase activity
J	0019213	molecular_function	deacetylase activity
J	0019899	molecular_function	enzyme binding
J	0042278	biological_process	purine nucleoside metabolic process
J	0046677	biological_process	response to antibiotic
J	0060698	molecular_function	endoribonuclease inhibitor activity
J	0061463	molecular_function	O-acetyl-ADP-ribose deacetylase activity
J	1900231	biological_process	regulation of single-species biofilm formation on inanimate substrate
K	0001883	molecular_function	purine nucleoside binding
K	0008428	molecular_function	ribonuclease inhibitor activity
K	0016787	molecular_function	hydrolase activity
K	0019213	molecular_function	deacetylase activity
K	0019899	molecular_function	enzyme binding
K	0042278	biological_process	purine nucleoside metabolic process
K	0046677	biological_process	response to antibiotic
K	0060698	molecular_function	endoribonuclease inhibitor activity
K	0061463	molecular_function	O-acetyl-ADP-ribose deacetylase activity
K	1900231	biological_process	regulation of single-species biofilm formation on inanimate substrate
L	0001883	molecular_function	purine nucleoside binding
L	0008428	molecular_function	ribonuclease inhibitor activity
L	0016787	molecular_function	hydrolase activity
L	0019213	molecular_function	deacetylase activity
L	0019899	molecular_function	enzyme binding
L	0042278	biological_process	purine nucleoside metabolic process
L	0046677	biological_process	response to antibiotic
L	0060698	molecular_function	endoribonuclease inhibitor activity
L	0061463	molecular_function	O-acetyl-ADP-ribose deacetylase activity
L	1900231	biological_process	regulation of single-species biofilm formation on inanimate substrate
M	0001883	molecular_function	purine nucleoside binding
M	0008428	molecular_function	ribonuclease inhibitor activity
M	0016787	molecular_function	hydrolase activity
M	0019213	molecular_function	deacetylase activity
M	0019899	molecular_function	enzyme binding
M	0042278	biological_process	purine nucleoside metabolic process
M	0046677	biological_process	response to antibiotic
M	0060698	molecular_function	endoribonuclease inhibitor activity
M	0061463	molecular_function	O-acetyl-ADP-ribose deacetylase activity
M	1900231	biological_process	regulation of single-species biofilm formation on inanimate substrate
N	0001883	molecular_function	purine nucleoside binding
N	0008428	molecular_function	ribonuclease inhibitor activity
N	0016787	molecular_function	hydrolase activity
N	0019213	molecular_function	deacetylase activity
N	0019899	molecular_function	enzyme binding
N	0042278	biological_process	purine nucleoside metabolic process
N	0046677	biological_process	response to antibiotic
N	0060698	molecular_function	endoribonuclease inhibitor activity
N	0061463	molecular_function	O-acetyl-ADP-ribose deacetylase activity
N	1900231	biological_process	regulation of single-species biofilm formation on inanimate substrate
O	0001883	molecular_function	purine nucleoside binding
O	0008428	molecular_function	ribonuclease inhibitor activity
O	0016787	molecular_function	hydrolase activity
O	0019213	molecular_function	deacetylase activity
O	0019899	molecular_function	enzyme binding
O	0042278	biological_process	purine nucleoside metabolic process
O	0046677	biological_process	response to antibiotic
O	0060698	molecular_function	endoribonuclease inhibitor activity
O	0061463	molecular_function	O-acetyl-ADP-ribose deacetylase activity
O	1900231	biological_process	regulation of single-species biofilm formation on inanimate substrate
P	0001883	molecular_function	purine nucleoside binding
P	0008428	molecular_function	ribonuclease inhibitor activity
P	0016787	molecular_function	hydrolase activity
P	0019213	molecular_function	deacetylase activity
P	0019899	molecular_function	enzyme binding
P	0042278	biological_process	purine nucleoside metabolic process
P	0046677	biological_process	response to antibiotic
P	0060698	molecular_function	endoribonuclease inhibitor activity
P	0061463	molecular_function	O-acetyl-ADP-ribose deacetylase activity
P	1900231	biological_process	regulation of single-species biofilm formation on inanimate substrate
Q	0001883	molecular_function	purine nucleoside binding
Q	0008428	molecular_function	ribonuclease inhibitor activity
Q	0016787	molecular_function	hydrolase activity
Q	0019213	molecular_function	deacetylase activity
Q	0019899	molecular_function	enzyme binding
Q	0042278	biological_process	purine nucleoside metabolic process
Q	0046677	biological_process	response to antibiotic
Q	0060698	molecular_function	endoribonuclease inhibitor activity
Q	0061463	molecular_function	O-acetyl-ADP-ribose deacetylase activity
Q	1900231	biological_process	regulation of single-species biofilm formation on inanimate substrate
R	0001883	molecular_function	purine nucleoside binding
R	0008428	molecular_function	ribonuclease inhibitor activity
R	0016787	molecular_function	hydrolase activity
R	0019213	molecular_function	deacetylase activity
R	0019899	molecular_function	enzyme binding
R	0042278	biological_process	purine nucleoside metabolic process
R	0046677	biological_process	response to antibiotic
R	0060698	molecular_function	endoribonuclease inhibitor activity
R	0061463	molecular_function	O-acetyl-ADP-ribose deacetylase activity
R	1900231	biological_process	regulation of single-species biofilm formation on inanimate substrate

Functional Information from PDB Data

site_id	AC1
Number of Residues	15
Details	binding site for residue APR R 201

Chain	Residue
R	ASP11
R	SER122
R	THR123
R	GLY124
R	VAL125
R	TYR126
R	TYR159
R	ILE12
R	ALA23
R	ALA25
R	GLY31
R	GLY32
R	GLY33
R	VAL34
R	ALA120

site_id	AC2
Number of Residues	6
Details	binding site for residue SO4 R 202

Chain	Residue
Q	ARG40
R	LEU102
R	ARG106
R	PHE144
R	ARG147
R	HIS148

site_id	AC3
Number of Residues	16
Details	binding site for residue APR A 201

Chain	Residue
A	ASP11
A	ILE12
A	ALA23
A	ALA25
A	GLY31
A	GLY32
A	GLY33
A	VAL34
A	ALA37
A	ALA120
A	SER122
A	THR123
A	GLY124
A	VAL125
A	TYR126
A	TYR159

site_id	AC4
Number of Residues	5
Details	binding site for residue SO4 A 202

Chain	Residue
A	ARG106
A	PHE144
A	ARG147
A	HIS148
F	ARG40

site_id	AC5
Number of Residues	17
Details	binding site for residue APR B 201

Chain	Residue
B	GLY10
B	ASP11
B	ILE12
B	ALA23
B	ALA25
B	GLY31
B	GLY32
B	GLY33
B	VAL34
B	ALA120
B	SER122
B	THR123
B	GLY124
B	VAL125
B	TYR126
B	TYR159
B	HOH303

site_id	AC6
Number of Residues	6
Details	binding site for residue SO4 B 202

Chain	Residue
B	LEU102
B	ARG106
B	PHE144
B	ARG147
B	HIS148
O	ARG40

site_id	AC7
Number of Residues	18
Details	binding site for residue APR C 201

Chain	Residue
C	ASP11
C	ILE12
C	ALA23
C	ALA25
C	GLY31
C	GLY32
C	GLY33
C	VAL34
C	ALA35
C	ALA37
C	ALA120
C	SER122
C	THR123
C	GLY124
C	VAL125
C	TYR126
C	TYR159
C	ACT203

site_id	AC8
Number of Residues	6
Details	binding site for residue SO4 C 202

Chain	Residue
C	LEU102
C	ARG106
C	PHE144
C	ARG147
C	HIS148
P	ARG40

site_id	AC9
Number of Residues	2
Details	binding site for residue ACT C 203

Chain	Residue
C	ALA25
C	APR201

site_id	AD1
Number of Residues	18
Details	binding site for residue APR D 201

Chain	Residue
D	VAL34
D	ALA120
D	ILE121
D	SER122
D	THR123
D	GLY124
D	VAL125
D	TYR126
D	TYR159
D	HOH301
D	ASP11
D	ILE12
D	ALA23
D	ALA25
D	GLY30
D	GLY31
D	GLY32
D	GLY33

site_id	AD2
Number of Residues	5
Details	binding site for residue SO4 D 202

Chain	Residue
D	ARG106
D	PHE144
D	ARG147
D	HIS148
M	ARG40

site_id	AD3
Number of Residues	14
Details	binding site for residue APR E 201

Chain	Residue
E	ASP11
E	ILE12
E	ALA23
E	ALA25
E	GLY32
E	GLY33
E	VAL34
E	ALA120
E	SER122
E	THR123
E	GLY124
E	VAL125
E	TYR126
E	TYR159

site_id	AD4
Number of Residues	5
Details	binding site for residue SO4 E 202

Chain	Residue
E	ARG106
E	PHE144
E	ARG147
E	HIS148
J	ARG40

site_id	AD5
Number of Residues	19
Details	binding site for residue ZOD F 201

Chain	Residue
F	GLY10
F	ASP11
F	ILE12
F	ALA25
F	GLY30
F	GLY31
F	GLY32
F	GLY33
F	VAL34
F	ALA35
F	ALA120
F	SER122
F	THR123
F	GLY124
F	VAL125
F	TYR126
F	VAL157
F	TYR159
F	HOH304

site_id	AD6
Number of Residues	7
Details	binding site for residue SO4 F 202

Chain	Residue
F	LEU102
F	ARG106
F	PHE144
F	ARG147
F	HIS148
F	HOH303
G	ARG40

site_id	AD7
Number of Residues	15
Details	binding site for residue APR G 201

Chain	Residue
G	ASP11
G	ILE12
G	ALA23
G	ALA25
G	GLY31
G	GLY32
G	GLY33
G	VAL34
G	ALA120
G	SER122
G	THR123
G	GLY124
G	VAL125
G	TYR126
G	TYR159

site_id	AD8
Number of Residues	6
Details	binding site for residue SO4 G 202

Chain	Residue
E	ARG40
G	LEU102
G	ARG106
G	PHE144
G	ARG147
G	HIS148

site_id	AD9
Number of Residues	15
Details	binding site for residue APR H 201

Chain	Residue
H	ASP11
H	ILE12
H	ALA23
H	GLY32
H	GLY33
H	VAL34
H	ALA35
H	ALA37
H	ALA120
H	SER122
H	THR123
H	GLY124
H	VAL125
H	TYR126
H	TYR159

site_id	AE1
Number of Residues	6
Details	binding site for residue SO4 H 202

Chain	Residue
C	ARG40
H	ARG106
H	PHE144
H	ARG147
H	HIS148
H	HOH305

site_id	AE2
Number of Residues	17
Details	binding site for residue APR I 201

Chain	Residue
I	GLY10
I	ASP11
I	ILE12
I	ALA23
I	GLY31
I	GLY32
I	GLY33
I	VAL34
I	ALA120
I	ILE121
I	SER122
I	THR123
I	GLY124
I	VAL125
I	TYR126
I	TYR159
I	HOH305

site_id	AE3
Number of Residues	5
Details	binding site for residue SO4 I 202

Chain	Residue
D	ARG40
I	ARG106
I	PHE144
I	ARG147
I	HIS148

site_id	AE4
Number of Residues	15
Details	binding site for residue APR J 201

Chain	Residue
J	ASP11
J	ILE12
J	ALA23
J	ALA25
J	GLY31
J	GLY32
J	GLY33
J	VAL34
J	ALA120
J	SER122
J	THR123
J	GLY124
J	VAL125
J	TYR126
J	TYR159

site_id	AE5
Number of Residues	6
Details	binding site for residue SO4 J 202

Chain	Residue
H	ARG40
J	LEU102
J	ARG106
J	PHE144
J	ARG147
J	HIS148

site_id	AE6
Number of Residues	1
Details	binding site for residue ACT J 203

Chain	Residue
J	TYR113

site_id	AE7
Number of Residues	18
Details	binding site for residue APR K 201

Chain	Residue
K	GLY10
K	ASP11
K	ILE12
K	ALA23
K	ALA25
K	GLY30
K	GLY31
K	GLY32
K	GLY33
K	VAL34
K	ALA35
K	ALA120
K	SER122
K	THR123
K	GLY124
K	VAL125
K	TYR126
K	TYR159

site_id	AE8
Number of Residues	4
Details	binding site for residue SO4 K 202

Chain	Residue
K	ARG106
K	ARG147
K	HIS148
L	ARG40

site_id	AE9
Number of Residues	15
Details	binding site for residue APR L 201

Chain	Residue
L	GLY10
L	ASP11
L	ILE12
L	ALA23
L	ALA25
L	GLY32
L	GLY33
L	VAL34
L	ALA120
L	SER122
L	THR123
L	GLY124
L	VAL125
L	TYR126
L	TYR159

site_id	AF1
Number of Residues	5
Details	binding site for residue SO4 L 202

Chain	Residue
A	ARG40
L	ARG106
L	PHE144
L	ARG147
L	HIS148

site_id	AF2
Number of Residues	19
Details	binding site for residue ZOD M 201

Chain	Residue
I	HOH311
M	GLY10
M	ASP11
M	ILE12
M	ALA23
M	ALA25
M	GLY30
M	GLY31
M	GLY32
M	GLY33
M	VAL34
M	ALA35
M	ALA120
M	SER122
M	THR123
M	GLY124
M	VAL125
M	TYR126
M	TYR159

site_id	AF3
Number of Residues	6
Details	binding site for residue SO4 M 202

Chain	Residue
M	ARG106
M	PHE144
M	ARG147
M	HIS148
M	HOH308
N	ARG40

site_id	AF4
Number of Residues	16
Details	binding site for residue APR N 201

Chain	Residue
N	GLY10
N	ASP11
N	ILE12
N	ALA23
N	ALA25
N	GLY32
N	GLY33
N	VAL34
N	ALA120
N	SER122
N	THR123
N	GLY124
N	VAL125
N	TYR126
N	TYR159
N	HOH302

site_id	AF5
Number of Residues	5
Details	binding site for residue SO4 N 202

Chain	Residue
B	ARG40
N	ARG106
N	PHE144
N	ARG147
N	HIS148

site_id	AF6
Number of Residues	14
Details	binding site for residue APR O 201

Chain	Residue
O	ASP11
O	ILE12
O	ALA23
O	ALA25
O	GLY32
O	GLY33
O	VAL34
O	ALA120
O	SER122
O	THR123
O	GLY124
O	VAL125
O	TYR126
O	TYR159

site_id	AF7
Number of Residues	5
Details	binding site for residue SO4 O 202

Chain	Residue
O	LEU102
O	ARG106
O	ARG147
O	HIS148
R	ARG40

site_id	AF8
Number of Residues	16
Details	binding site for residue APR P 201

Chain	Residue
P	GLY10
P	ASP11
P	ILE12
P	ALA23
P	ALA25
P	GLY32
P	VAL34
P	ALA35
P	ALA37
P	ALA120
P	SER122
P	THR123
P	GLY124
P	VAL125
P	TYR126
P	TYR159

site_id	AF9
Number of Residues	6
Details	binding site for residue SO4 P 202

Chain	Residue
I	ARG40
P	LEU102
P	ARG106
P	PHE144
P	ARG147
P	HIS148

site_id	AG1
Number of Residues	3
Details	binding site for residue ACT Q 401

Chain	Residue
E	GLY31
Q	ALA25
Q	TYR126

site_id	AG2
Number of Residues	16
Details	binding site for residue APR Q 402

Chain	Residue
Q	GLY10
Q	ASP11
Q	ILE12
Q	ALA23
Q	ALA25
Q	GLY31
Q	GLY32
Q	GLY33
Q	VAL34
Q	ALA120
Q	SER122
Q	THR123
Q	GLY124
Q	VAL125
Q	TYR126
Q	TYR159

site_id	AG3
Number of Residues	5
Details	binding site for residue SO4 Q 403

Chain	Residue
K	ARG40
Q	ARG106
Q	PHE144
Q	ARG147
Q	HIS148

Functional Information from SwissProt/UniProt

site_id	SWS_FT_FI1
Number of Residues	18
Details	Active site: {"description":"Proton acceptor","evidences":[{"source":"HAMAP-Rule","id":"MF_01205","evidenceCode":"ECO:0000255"},{"source":"PubMed","id":"26481419","evidenceCode":"ECO:0000305"}]}

Chain

Residue

Details

site_id	SWS_FT_FI2
Number of Residues	144
Details	Binding site: {"evidences":[{"source":"HAMAP-Rule","id":"MF_01205","evidenceCode":"ECO:0000255"},{"source":"PubMed","id":"26481419","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

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