Summary Structural details Experimental details Functional details Sequence Neighbor History Downloads

5CMS

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	16
Details	binding site for residue APR R 401

Chain	Residue
R	ASP11
R	ALA120
R	SER122
R	THR123
R	GLY124
R	VAL125
R	ALA126
R	TYR159
R	ILE12
R	ALA23
R	ALA24
R	ASN25
R	GLY33
R	VAL34
R	GLY83
R	VAL85

site_id	AC2
Number of Residues	6
Details	binding site for residue SO4 R 402

Chain	Residue
Q	ARG40
R	ARG106
R	PHE144
R	ARG147
R	HIS148
R	HOH501

site_id	AC3
Number of Residues	18
Details	binding site for residue APR A 201

Chain	Residue
A	ASP11
A	ILE12
A	ALA23
A	ALA24
A	ASN25
A	PRO26
A	GLY32
A	GLY33
A	VAL34
A	ALA37
A	VAL85
A	ALA120
A	SER122
A	THR123
A	GLY124
A	VAL125
A	ALA126
A	TYR159

site_id	AC4
Number of Residues	7
Details	binding site for residue SO4 A 202

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

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

Chain	Residue
B	GLY10
B	ASP11
B	ILE12
B	ALA24
B	ASN25
B	GLY32
B	GLY33
B	VAL34
B	ALA37
B	VAL85
B	ALA120
B	SER122
B	THR123
B	GLY124
B	VAL125
B	ALA126
B	TYR159

site_id	AC6
Number of Residues	5
Details	binding site for residue SO4 B 202

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

site_id	AC7
Number of Residues	14
Details	binding site for residue APR C 201

Chain	Residue
C	ASP11
C	ILE12
C	ALA24
C	ASN25
C	GLY33
C	VAL34
C	VAL85
C	ALA120
C	SER122
C	THR123
C	GLY124
C	VAL125
C	ALA126
C	TYR159

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	12
Details	binding site for residue APR D 201

Chain	Residue
D	VAL125
D	ALA126
D	ASP11
D	ILE12
D	ALA23
D	GLY33
D	VAL34
D	ALA37
D	ALA120
D	SER122
D	THR123
D	GLY124

site_id	AD1
Number of Residues	6
Details	binding site for residue SO4 D 202

Chain	Residue
D	LEU102
D	ARG106
D	PHE144
D	ARG147
D	HIS148
M	ARG40

site_id	AD2
Number of Residues	14
Details	binding site for residue APR E 201

Chain	Residue
E	GLY10
E	ASP11
E	ILE12
E	ASN25
E	GLY33
E	VAL34
E	VAL85
E	ALA120
E	SER122
E	THR123
E	GLY124
E	VAL125
E	ALA126
E	TYR159

site_id	AD3
Number of Residues	6
Details	binding site for residue SO4 E 202

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

site_id	AD4
Number of Residues	16
Details	binding site for residue APR F 201

Chain	Residue
F	GLY10
F	ASP11
F	ILE12
F	ALA24
F	ASN25
F	GLY33
F	VAL34
F	GLY83
F	ALA120
F	SER122
F	THR123
F	GLY124
F	VAL125
F	ALA126
F	VAL157
F	TYR159

site_id	AD5
Number of Residues	6
Details	binding site for residue SO4 F 202

Chain	Residue
F	ARG106
F	PHE144
F	ARG147
F	HIS148
F	HOH301
G	ARG40

site_id	AD6
Number of Residues	11
Details	binding site for residue APR G 201

Chain	Residue
G	ASP11
G	ILE12
G	GLY33
G	VAL34
G	ALA120
G	SER122
G	THR123
G	GLY124
G	VAL125
G	ALA126
G	TYR159

site_id	AD7
Number of Residues	5
Details	binding site for residue SO4 G 202

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

site_id	AD8
Number of Residues	17
Details	binding site for residue APR H 201

Chain	Residue
H	GLY10
H	ASP11
H	ILE12
H	ALA23
H	ALA24
H	ASN25
H	GLY33
H	VAL34
H	GLY83
H	VAL85
H	ALA120
H	SER122
H	THR123
H	GLY124
H	VAL125
H	ALA126
H	TYR159

site_id	AD9
Number of Residues	6
Details	binding site for residue SO4 H 202

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

site_id	AE1
Number of Residues	13
Details	binding site for residue APR I 201

Chain	Residue
I	ASP11
I	ILE12
I	ALA23
I	GLY33
I	VAL34
I	ALA120
I	ILE121
I	SER122
I	THR123
I	GLY124
I	VAL125
I	ALA126
I	TYR159

site_id	AE2
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	AE3
Number of Residues	17
Details	binding site for residue APR J 201

Chain	Residue
J	GLY10
J	ASP11
J	ILE12
J	ALA24
J	ASN25
J	GLY32
J	GLY33
J	VAL34
J	ALA120
J	ILE121
J	SER122
J	THR123
J	GLY124
J	VAL125
J	ALA126
J	TYR159
J	HOH301

site_id	AE4
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	AE5
Number of Residues	16
Details	binding site for residue APR K 201

Chain	Residue
K	GLY10
K	ASP11
K	ILE12
K	ASN25
K	GLY32
K	GLY33
K	VAL34
K	ALA37
K	GLY83
K	ALA120
K	SER122
K	THR123
K	GLY124
K	VAL125
K	ALA126
K	TYR159

site_id	AE6
Number of Residues	5
Details	binding site for residue SO4 K 202

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

site_id	AE7
Number of Residues	15
Details	binding site for residue APR L 201

Chain	Residue
L	GLY10
L	ASP11
L	ILE12
L	ASN25
L	GLY33
L	VAL34
L	VAL85
L	ALA120
L	ILE121
L	SER122
L	THR123
L	GLY124
L	VAL125
L	ALA126
L	TYR159

site_id	AE8
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	AE9
Number of Residues	14
Details	binding site for residue APR M 201

Chain	Residue
M	ASP11
M	ILE12
M	ASN25
M	GLY33
M	VAL34
M	GLY83
M	VAL85
M	ALA120
M	SER122
M	THR123
M	GLY124
M	VAL125
M	ALA126
M	TYR159

site_id	AF1
Number of Residues	7
Details	binding site for residue SO4 M 202

Chain	Residue
M	ARG106
M	PHE144
M	ARG147
M	HIS148
M	HOH305
N	ARG40
N	HOH301

site_id	AF2
Number of Residues	14
Details	binding site for residue APR N 201

Chain	Residue
N	ASP11
N	ILE12
N	ALA23
N	ASN25
N	GLY33
N	VAL34
N	VAL85
N	ALA120
N	SER122
N	THR123
N	GLY124
N	VAL125
N	ALA126
N	TYR159

site_id	AF3
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	AF4
Number of Residues	18
Details	binding site for residue APR O 201

Chain	Residue
O	GLY10
O	ASP11
O	ILE12
O	ALA23
O	ALA24
O	ASN25
O	GLY32
O	GLY33
O	VAL34
O	GLY83
O	ALA120
O	ILE121
O	SER122
O	THR123
O	GLY124
O	VAL125
O	ALA126
O	TYR159

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

Chain	Residue
O	ARG106
O	PHE144
O	ARG147
O	HIS148
R	ARG40

site_id	AF6
Number of Residues	18
Details	binding site for residue APR P 201

Chain	Residue
P	GLY10
P	ASP11
P	ILE12
P	ALA23
P	ALA24
P	ASN25
P	GLY33
P	VAL34
P	GLY83
P	VAL85
P	ALA120
P	ILE121
P	SER122
P	THR123
P	GLY124
P	VAL125
P	ALA126
P	TYR159

site_id	AF7
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	AF8
Number of Residues	18
Details	binding site for residue APR Q 201

Chain	Residue
Q	GLY10
Q	ASP11
Q	ILE12
Q	ALA23
Q	ALA24
Q	ASN25
Q	GLY32
Q	GLY33
Q	VAL34
Q	ALA37
Q	GLY83
Q	ALA120
Q	SER122
Q	THR123
Q	GLY124
Q	VAL125
Q	ALA126
Q	TYR159

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

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

Functional Information from SwissProt/UniProt

site_id	SWS_FT_FI1
Number of Residues	18
Details	ACT_SITE: Proton acceptor => ECO:0000255\|HAMAP-Rule:MF_01205, ECO:0000305\|PubMed:26481419

Chain	Residue	Details
R	ASP35
I	ASP35
J	ASP35
K	ASP35
L	ASP35
M	ASP35
N	ASP35
O	ASP35
P	ASP35
Q	ASP35
A	ASP35
B	ASP35
C	ASP35
D	ASP35
E	ASP35
F	ASP35
G	ASP35
H	ASP35

site_id	SWS_FT_FI2
Number of Residues	72
Details	BINDING: BINDING => ECO:0000255\|HAMAP-Rule:MF_01205, ECO:0000269\|PubMed:26481419

Chain	Residue	Details
R	ASP11
B	ASN25
B	GLY33
B	SER122
C	ASP11
C	ASN25
C	GLY33
C	SER122
D	ASP11
D	ASN25
D	GLY33
R	ASN25
D	SER122
E	ASP11
E	ASN25
E	GLY33
E	SER122
F	ASP11
F	ASN25
F	GLY33
F	SER122
G	ASP11
R	GLY33
G	ASN25
G	GLY33
G	SER122
H	ASP11
H	ASN25
H	GLY33
H	SER122
I	ASP11
I	ASN25
I	GLY33
R	SER122
I	SER122
J	ASP11
J	ASN25
J	GLY33
J	SER122
K	ASP11
K	ASN25
K	GLY33
K	SER122
L	ASP11
A	ASP11
L	ASN25
L	GLY33
L	SER122
M	ASP11
M	ASN25
M	GLY33
M	SER122
N	ASP11
N	ASN25
N	GLY33
A	ASN25
N	SER122
O	ASP11
O	ASN25
O	GLY33
O	SER122
P	ASP11
P	ASN25
P	GLY33
P	SER122
Q	ASP11
A	GLY33
Q	ASN25
Q	GLY33
Q	SER122
A	SER122
B	ASP11

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