Summary Structural details Experimental details Functional details Sequence Neighbor History Downloads

3SHD

Crystal structure of Nudix hydrolase Orf153, ymfB, from Escherichia coli K-1

Functional Information from GO Data

Chain	GOid	namespace	contents
A	0004787	molecular_function	thiamine diphosphate phosphatase activity
A	0016787	molecular_function	hydrolase activity
A	0017110	molecular_function	nucleoside diphosphate phosphatase activity
A	0017111	molecular_function	ribonucleoside triphosphate phosphatase activity
B	0004787	molecular_function	thiamine diphosphate phosphatase activity
B	0016787	molecular_function	hydrolase activity
B	0017110	molecular_function	nucleoside diphosphate phosphatase activity
B	0017111	molecular_function	ribonucleoside triphosphate phosphatase activity
C	0004787	molecular_function	thiamine diphosphate phosphatase activity
C	0016787	molecular_function	hydrolase activity
C	0017110	molecular_function	nucleoside diphosphate phosphatase activity
C	0017111	molecular_function	ribonucleoside triphosphate phosphatase activity
D	0004787	molecular_function	thiamine diphosphate phosphatase activity
D	0016787	molecular_function	hydrolase activity
D	0017110	molecular_function	nucleoside diphosphate phosphatase activity
D	0017111	molecular_function	ribonucleoside triphosphate phosphatase activity
E	0004787	molecular_function	thiamine diphosphate phosphatase activity
E	0016787	molecular_function	hydrolase activity
E	0017110	molecular_function	nucleoside diphosphate phosphatase activity
E	0017111	molecular_function	ribonucleoside triphosphate phosphatase activity
F	0004787	molecular_function	thiamine diphosphate phosphatase activity
F	0016787	molecular_function	hydrolase activity
F	0017110	molecular_function	nucleoside diphosphate phosphatase activity
F	0017111	molecular_function	ribonucleoside triphosphate phosphatase activity
G	0004787	molecular_function	thiamine diphosphate phosphatase activity
G	0016787	molecular_function	hydrolase activity
G	0017110	molecular_function	nucleoside diphosphate phosphatase activity
G	0017111	molecular_function	ribonucleoside triphosphate phosphatase activity
H	0004787	molecular_function	thiamine diphosphate phosphatase activity
H	0016787	molecular_function	hydrolase activity
H	0017110	molecular_function	nucleoside diphosphate phosphatase activity
H	0017111	molecular_function	ribonucleoside triphosphate phosphatase activity
I	0004787	molecular_function	thiamine diphosphate phosphatase activity
I	0016787	molecular_function	hydrolase activity
I	0017110	molecular_function	nucleoside diphosphate phosphatase activity
I	0017111	molecular_function	ribonucleoside triphosphate phosphatase activity
J	0004787	molecular_function	thiamine diphosphate phosphatase activity
J	0016787	molecular_function	hydrolase activity
J	0017110	molecular_function	nucleoside diphosphate phosphatase activity
J	0017111	molecular_function	ribonucleoside triphosphate phosphatase activity
K	0004787	molecular_function	thiamine diphosphate phosphatase activity
K	0016787	molecular_function	hydrolase activity
K	0017110	molecular_function	nucleoside diphosphate phosphatase activity
K	0017111	molecular_function	ribonucleoside triphosphate phosphatase activity
L	0004787	molecular_function	thiamine diphosphate phosphatase activity
L	0016787	molecular_function	hydrolase activity
L	0017110	molecular_function	nucleoside diphosphate phosphatase activity
L	0017111	molecular_function	ribonucleoside triphosphate phosphatase activity

Functional Information from PDB Data

site_id	AC1
Number of Residues	8
Details	BINDING SITE FOR RESIDUE MN A 154

Chain	Residue
A	GLU51
A	GLU55
A	MN155
A	SO4156
A	SO4157
A	HOH160
A	HOH162
A	HOH163

site_id	AC2
Number of Residues	7
Details	BINDING SITE FOR RESIDUE MN A 155

Chain	Residue
A	MN154
A	SO4156
A	HOH159
A	HOH163
A	HOH164
A	HOH166
A	GLU51

site_id	AC3
Number of Residues	11
Details	BINDING SITE FOR RESIDUE SO4 A 156

Chain	Residue
A	ALA35
A	GLY36
A	HIS37
A	GLU51
A	MN154
A	MN155
A	SO4157
A	HOH163
A	HOH164
A	HOH165
A	HOH166

site_id	AC4
Number of Residues	10
Details	BINDING SITE FOR RESIDUE SO4 A 157

Chain	Residue
A	GLU23
A	ASN32
A	ALA35
A	GLY36
A	GLU51
A	GLU55
A	MN154
A	SO4156
A	SO4158
A	HOH162

site_id	AC5
Number of Residues	6
Details	BINDING SITE FOR RESIDUE SO4 A 158

Chain	Residue
A	THR7
A	ASN32
A	ALA35
A	GLY36
A	ARG81
A	SO4157

site_id	AC6
Number of Residues	4
Details	BINDING SITE FOR RESIDUE MN B 154

Chain	Residue
B	GLU51
B	GLU55
B	SO4156
B	SO4157

site_id	AC7
Number of Residues	3
Details	BINDING SITE FOR RESIDUE MN B 155

Chain	Residue
B	GLU51
B	SO4156
B	HOH177

site_id	AC8
Number of Residues	8
Details	BINDING SITE FOR RESIDUE SO4 B 156

Chain	Residue
B	GLY36
B	HIS37
B	GLU51
B	MN154
B	MN155
B	SO4157
B	HOH161
B	HOH213

site_id	AC9
Number of Residues	8
Details	BINDING SITE FOR RESIDUE SO4 B 157

Chain	Residue
B	GLU23
B	ALA35
B	GLY36
B	GLU51
B	GLU55
B	MN154
B	SO4156
B	SO4158

site_id	BC1
Number of Residues	6
Details	BINDING SITE FOR RESIDUE SO4 B 158

Chain	Residue
B	THR7
B	ASN32
B	ALA35
B	GLY36
B	ARG81
B	SO4157

site_id	BC2
Number of Residues	5
Details	BINDING SITE FOR RESIDUE MN C 154

Chain	Residue
C	GLU51
C	GLU55
C	MN155
C	SO4156
C	SO4157

site_id	BC3
Number of Residues	4
Details	BINDING SITE FOR RESIDUE MN C 155

Chain	Residue
C	GLU51
C	MN154
C	SO4156
C	HOH269

site_id	BC4
Number of Residues	8
Details	BINDING SITE FOR RESIDUE SO4 C 156

Chain	Residue
C	GLY36
C	HIS37
C	GLU51
C	MN154
C	MN155
C	SO4157
C	HOH250
C	HOH269

site_id	BC5
Number of Residues	8
Details	BINDING SITE FOR RESIDUE SO4 C 157

Chain	Residue
C	GLU23
C	ALA35
C	GLY36
C	GLU51
C	GLU55
C	MN154
C	SO4156
C	SO4158

site_id	BC6
Number of Residues	6
Details	BINDING SITE FOR RESIDUE SO4 C 158

Chain	Residue
C	GLY36
C	ARG81
C	SO4157
C	THR7
C	ASN32
C	ALA35

site_id	BC7
Number of Residues	2
Details	BINDING SITE FOR RESIDUE MN D 154

Chain	Residue
D	GLU51
D	SO4156

site_id	BC8
Number of Residues	4
Details	BINDING SITE FOR RESIDUE MN D 155

Chain	Residue
D	GLU51
D	GLU55
D	SO4156
D	SO4157

site_id	BC9
Number of Residues	8
Details	BINDING SITE FOR RESIDUE SO4 D 156

Chain	Residue
D	GLY36
D	HIS37
D	GLU51
D	GLU55
D	MN154
D	MN155
D	SO4157
D	HOH252

site_id	CC1
Number of Residues	10
Details	BINDING SITE FOR RESIDUE SO4 D 157

Chain	Residue
D	GLU23
D	ASN32
D	ALA35
D	GLY36
D	GLU51
D	GLU55
D	ARG119
D	MN155
D	SO4156
D	SO4158

site_id	CC2
Number of Residues	6
Details	BINDING SITE FOR RESIDUE SO4 D 158

Chain	Residue
D	THR7
D	ASN32
D	ALA35
D	GLY36
D	ARG81
D	SO4157

site_id	CC3
Number of Residues	4
Details	BINDING SITE FOR RESIDUE MN E 154

Chain	Residue
E	GLU51
E	MN155
E	SO4156
E	HOH172

site_id	CC4
Number of Residues	5
Details	BINDING SITE FOR RESIDUE MN E 155

Chain	Residue
E	GLU51
E	GLU55
E	MN154
E	SO4156
E	SO4157

site_id	CC5
Number of Residues	9
Details	BINDING SITE FOR RESIDUE SO4 E 156

Chain	Residue
E	ALA35
E	GLY36
E	HIS37
E	GLU51
E	MN154
E	MN155
E	SO4157
E	HOH171
E	HOH172

site_id	CC6
Number of Residues	8
Details	BINDING SITE FOR RESIDUE SO4 E 157

Chain	Residue
E	GLU23
E	ALA35
E	GLY36
E	GLU51
E	GLU55
E	MN155
E	SO4156
E	SO4158

site_id	CC7
Number of Residues	7
Details	BINDING SITE FOR RESIDUE SO4 E 158

Chain	Residue
E	THR7
E	ASN32
E	ALA35
E	GLY36
E	ARG81
E	SO4157
E	HOH235

site_id	CC8
Number of Residues	5
Details	BINDING SITE FOR RESIDUE MN F 154

Chain	Residue
F	GLU51
F	GLU55
F	MN155
F	SO4156
F	SO4157

site_id	CC9
Number of Residues	3
Details	BINDING SITE FOR RESIDUE MN F 155

Chain	Residue
F	GLU51
F	MN154
F	SO4156

site_id	DC1
Number of Residues	6
Details	BINDING SITE FOR RESIDUE SO4 F 156

Chain	Residue
F	GLY36
F	HIS37
F	GLU51
F	MN154
F	MN155
F	SO4157

site_id	DC2
Number of Residues	10
Details	BINDING SITE FOR RESIDUE SO4 F 157

Chain	Residue
F	GLU23
F	ALA35
F	GLY36
F	GLU51
F	GLU55
F	ARG119
F	MN154
F	SO4156
F	SO4158
F	HOH169

site_id	DC3
Number of Residues	6
Details	BINDING SITE FOR RESIDUE SO4 F 158

Chain	Residue
F	THR7
F	ASN32
F	ALA35
F	GLY36
F	ARG81
F	SO4157

site_id	DC4
Number of Residues	6
Details	BINDING SITE FOR RESIDUE MN G 154

Chain	Residue
G	GLU51
G	GLU54
G	GLU55
G	MN155
G	SO4156
G	SO4158

site_id	DC5
Number of Residues	3
Details	BINDING SITE FOR RESIDUE MN G 155

Chain	Residue
G	GLU51
G	MN154
G	SO4156

site_id	DC6
Number of Residues	6
Details	BINDING SITE FOR RESIDUE SO4 G 156

Chain	Residue
G	GLY36
G	HIS37
G	GLU51
G	MN154
G	MN155
G	SO4158

site_id	DC7
Number of Residues	6
Details	BINDING SITE FOR RESIDUE SO4 G 157

Chain	Residue
G	THR7
G	ASN32
G	ALA35
G	GLY36
G	ARG81
G	SO4158

site_id	DC8
Number of Residues	9
Details	BINDING SITE FOR RESIDUE SO4 G 158

Chain	Residue
G	GLU23
G	ALA35
G	GLY36
G	GLU51
G	GLU55
G	MN154
G	SO4156
G	SO4157
G	HOH168

site_id	DC9
Number of Residues	4
Details	BINDING SITE FOR RESIDUE MN H 154

Chain	Residue
H	GLU51
H	GLU55
H	SO4156
H	SO4157

site_id	EC1
Number of Residues	2
Details	BINDING SITE FOR RESIDUE MN H 155

Chain	Residue
H	GLU51
H	SO4156

site_id	EC2
Number of Residues	9
Details	BINDING SITE FOR RESIDUE SO4 H 156

Chain	Residue
H	GLY36
H	HIS37
H	GLU51
H	GLU55
H	MN154
H	MN155
H	SO4157
H	HOH160
H	HOH162

site_id	EC3
Number of Residues	9
Details	BINDING SITE FOR RESIDUE SO4 H 157

Chain	Residue
H	GLU23
H	ASN32
H	ALA35
H	GLY36
H	GLU51
H	GLU55
H	MN154
H	SO4156
H	SO4158

site_id	EC4
Number of Residues	6
Details	BINDING SITE FOR RESIDUE SO4 H 158

Chain	Residue
H	THR7
H	ASN32
H	ALA35
H	GLY36
H	ARG81
H	SO4157

site_id	EC5
Number of Residues	5
Details	BINDING SITE FOR RESIDUE MN I 154

Chain	Residue
I	GLU51
I	GLU55
I	MN155
I	SO4156
I	SO4157

site_id	EC6
Number of Residues	5
Details	BINDING SITE FOR RESIDUE MN I 155

Chain	Residue
I	ARG50
I	GLU51
I	GLU54
I	MN154
I	SO4156

site_id	EC7
Number of Residues	5
Details	BINDING SITE FOR RESIDUE SO4 I 156

Chain	Residue
I	HIS37
I	GLU51
I	MN154
I	MN155
I	SO4157

site_id	EC8
Number of Residues	6
Details	BINDING SITE FOR RESIDUE SO4 I 157

Chain	Residue
I	ALA35
I	GLY36
I	GLU55
I	MN154
I	SO4156
I	SO4158

site_id	EC9
Number of Residues	5
Details	BINDING SITE FOR RESIDUE SO4 I 158

Chain	Residue
I	THR7
I	ASN32
I	ALA35
I	ARG81
I	SO4157

site_id	FC1
Number of Residues	5
Details	BINDING SITE FOR RESIDUE MN J 154

Chain	Residue
J	GLU51
J	GLU55
J	MN155
J	SO4156
J	SO4157

site_id	FC2
Number of Residues	4
Details	BINDING SITE FOR RESIDUE MN J 155

Chain	Residue
J	GLU51
J	MN154
J	SO4156
J	HOH267

site_id	FC3
Number of Residues	7
Details	BINDING SITE FOR RESIDUE SO4 J 156

Chain	Residue
J	GLY36
J	HIS37
J	GLU51
J	MN154
J	MN155
J	SO4157
J	HOH175

site_id	FC4
Number of Residues	9
Details	BINDING SITE FOR RESIDUE SO4 J 157

Chain	Residue
J	GLU23
J	ALA35
J	GLY36
J	GLU51
J	GLU55
J	MN154
J	SO4156
J	SO4158
J	HOH175

site_id	FC5
Number of Residues	6
Details	BINDING SITE FOR RESIDUE SO4 J 158

Chain	Residue
J	THR7
J	ASN32
J	ALA35
J	GLY36
J	ARG81
J	SO4157

site_id	FC6
Number of Residues	7
Details	BINDING SITE FOR RESIDUE MN K 154

Chain	Residue
K	GLU51
K	GLU55
K	MN155
K	SO4156
K	SO4157
K	HOH178
K	HOH204

site_id	FC7
Number of Residues	3
Details	BINDING SITE FOR RESIDUE MN K 155

Chain	Residue
K	GLU51
K	MN154
K	SO4156

site_id	FC8
Number of Residues	7
Details	BINDING SITE FOR RESIDUE SO4 K 156

Chain	Residue
K	GLY36
K	HIS37
K	GLU51
K	MN154
K	MN155
K	SO4157
K	HOH172

site_id	FC9
Number of Residues	10
Details	BINDING SITE FOR RESIDUE SO4 K 157

Chain	Residue
K	GLU23
K	ASN32
K	ALA35
K	GLY36
K	GLU51
K	GLU55
K	MN154
K	SO4156
K	SO4158
K	HOH178

site_id	GC1
Number of Residues	6
Details	BINDING SITE FOR RESIDUE SO4 K 158

Chain	Residue
K	THR7
K	ASN32
K	ALA35
K	GLY36
K	ARG81
K	SO4157

site_id	GC2
Number of Residues	3
Details	BINDING SITE FOR RESIDUE MN L 154

Chain	Residue
L	GLU51
L	MN155
L	SO4156

site_id	GC3
Number of Residues	6
Details	BINDING SITE FOR RESIDUE MN L 155

Chain	Residue
L	GLU51
L	GLU54
L	GLU55
L	MN154
L	SO4156
L	SO4157

site_id	GC4
Number of Residues	7
Details	BINDING SITE FOR RESIDUE SO4 L 156

Chain	Residue
L	GLY36
L	HIS37
L	GLU51
L	MN154
L	MN155
L	SO4157
L	HOH173

site_id	GC5
Number of Residues	9
Details	BINDING SITE FOR RESIDUE SO4 L 157

Chain	Residue
L	GLU23
L	ALA35
L	GLY36
L	GLU51
L	GLU55
L	MN155
L	SO4156
L	SO4158
L	HOH173

site_id	GC6
Number of Residues	4
Details	BINDING SITE FOR RESIDUE SO4 L 158

Chain	Residue
L	THR7
L	ASN32
L	ARG81
L	SO4157

Functional Information from PROSITE/UniProt

site_id	PS00893
Number of Residues	22
Details	NUDIX_BOX Nudix box signature. GhleadEtlveAAaRELwEEtG

Chain	Residue	Details
A	GLY36-GLY57

Functional Information from SwissProt/UniProt

site_id	SWS_FT_FI1
Number of Residues	1536
Details	Domain: {"description":"Nudix hydrolase","evidences":[{"source":"PROSITE-ProRule","id":"PRU00794","evidenceCode":"ECO:0000255"}]}

Chain

Residue

Details

site_id	SWS_FT_FI2
Number of Residues	252
Details	Motif: {"description":"Nudix box"}

Chain

Residue

Details

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