Summary Structural details Experimental details Functional details Sequence Neighbor History Downloads

2R8Z

Crystal structure of YrbI phosphatase from Escherichia coli in complex with a phosphate and a calcium ion

Functional Information from GO Data

Chain	GOid	namespace	contents
A	0008781	molecular_function	N-acylneuraminate cytidylyltransferase activity
A	0009103	biological_process	lipopolysaccharide biosynthetic process
A	0016787	molecular_function	hydrolase activity
A	0016788	molecular_function	hydrolase activity, acting on ester bonds
A	0019143	molecular_function	3-deoxy-manno-octulosonate-8-phosphatase activity
A	0046872	molecular_function	metal ion binding
B	0008781	molecular_function	N-acylneuraminate cytidylyltransferase activity
B	0009103	biological_process	lipopolysaccharide biosynthetic process
B	0016787	molecular_function	hydrolase activity
B	0016788	molecular_function	hydrolase activity, acting on ester bonds
B	0019143	molecular_function	3-deoxy-manno-octulosonate-8-phosphatase activity
B	0046872	molecular_function	metal ion binding
C	0008781	molecular_function	N-acylneuraminate cytidylyltransferase activity
C	0009103	biological_process	lipopolysaccharide biosynthetic process
C	0016787	molecular_function	hydrolase activity
C	0016788	molecular_function	hydrolase activity, acting on ester bonds
C	0019143	molecular_function	3-deoxy-manno-octulosonate-8-phosphatase activity
C	0046872	molecular_function	metal ion binding
D	0008781	molecular_function	N-acylneuraminate cytidylyltransferase activity
D	0009103	biological_process	lipopolysaccharide biosynthetic process
D	0016787	molecular_function	hydrolase activity
D	0016788	molecular_function	hydrolase activity, acting on ester bonds
D	0019143	molecular_function	3-deoxy-manno-octulosonate-8-phosphatase activity
D	0046872	molecular_function	metal ion binding
E	0008781	molecular_function	N-acylneuraminate cytidylyltransferase activity
E	0009103	biological_process	lipopolysaccharide biosynthetic process
E	0016787	molecular_function	hydrolase activity
E	0016788	molecular_function	hydrolase activity, acting on ester bonds
E	0019143	molecular_function	3-deoxy-manno-octulosonate-8-phosphatase activity
E	0046872	molecular_function	metal ion binding
F	0008781	molecular_function	N-acylneuraminate cytidylyltransferase activity
F	0009103	biological_process	lipopolysaccharide biosynthetic process
F	0016787	molecular_function	hydrolase activity
F	0016788	molecular_function	hydrolase activity, acting on ester bonds
F	0019143	molecular_function	3-deoxy-manno-octulosonate-8-phosphatase activity
F	0046872	molecular_function	metal ion binding
G	0008781	molecular_function	N-acylneuraminate cytidylyltransferase activity
G	0009103	biological_process	lipopolysaccharide biosynthetic process
G	0016787	molecular_function	hydrolase activity
G	0016788	molecular_function	hydrolase activity, acting on ester bonds
G	0019143	molecular_function	3-deoxy-manno-octulosonate-8-phosphatase activity
G	0046872	molecular_function	metal ion binding
H	0008781	molecular_function	N-acylneuraminate cytidylyltransferase activity
H	0009103	biological_process	lipopolysaccharide biosynthetic process
H	0016787	molecular_function	hydrolase activity
H	0016788	molecular_function	hydrolase activity, acting on ester bonds
H	0019143	molecular_function	3-deoxy-manno-octulosonate-8-phosphatase activity
H	0046872	molecular_function	metal ion binding
I	0008781	molecular_function	N-acylneuraminate cytidylyltransferase activity
I	0009103	biological_process	lipopolysaccharide biosynthetic process
I	0016787	molecular_function	hydrolase activity
I	0016788	molecular_function	hydrolase activity, acting on ester bonds
I	0019143	molecular_function	3-deoxy-manno-octulosonate-8-phosphatase activity
I	0046872	molecular_function	metal ion binding
J	0008781	molecular_function	N-acylneuraminate cytidylyltransferase activity
J	0009103	biological_process	lipopolysaccharide biosynthetic process
J	0016787	molecular_function	hydrolase activity
J	0016788	molecular_function	hydrolase activity, acting on ester bonds
J	0019143	molecular_function	3-deoxy-manno-octulosonate-8-phosphatase activity
J	0046872	molecular_function	metal ion binding
K	0008781	molecular_function	N-acylneuraminate cytidylyltransferase activity
K	0009103	biological_process	lipopolysaccharide biosynthetic process
K	0016787	molecular_function	hydrolase activity
K	0016788	molecular_function	hydrolase activity, acting on ester bonds
K	0019143	molecular_function	3-deoxy-manno-octulosonate-8-phosphatase activity
K	0046872	molecular_function	metal ion binding
L	0008781	molecular_function	N-acylneuraminate cytidylyltransferase activity
L	0009103	biological_process	lipopolysaccharide biosynthetic process
L	0016787	molecular_function	hydrolase activity
L	0016788	molecular_function	hydrolase activity, acting on ester bonds
L	0019143	molecular_function	3-deoxy-manno-octulosonate-8-phosphatase activity
L	0046872	molecular_function	metal ion binding
M	0008781	molecular_function	N-acylneuraminate cytidylyltransferase activity
M	0009103	biological_process	lipopolysaccharide biosynthetic process
M	0016787	molecular_function	hydrolase activity
M	0016788	molecular_function	hydrolase activity, acting on ester bonds
M	0019143	molecular_function	3-deoxy-manno-octulosonate-8-phosphatase activity
M	0046872	molecular_function	metal ion binding
N	0008781	molecular_function	N-acylneuraminate cytidylyltransferase activity
N	0009103	biological_process	lipopolysaccharide biosynthetic process
N	0016787	molecular_function	hydrolase activity
N	0016788	molecular_function	hydrolase activity, acting on ester bonds
N	0019143	molecular_function	3-deoxy-manno-octulosonate-8-phosphatase activity
N	0046872	molecular_function	metal ion binding
O	0008781	molecular_function	N-acylneuraminate cytidylyltransferase activity
O	0009103	biological_process	lipopolysaccharide biosynthetic process
O	0016787	molecular_function	hydrolase activity
O	0016788	molecular_function	hydrolase activity, acting on ester bonds
O	0019143	molecular_function	3-deoxy-manno-octulosonate-8-phosphatase activity
O	0046872	molecular_function	metal ion binding
P	0008781	molecular_function	N-acylneuraminate cytidylyltransferase activity
P	0009103	biological_process	lipopolysaccharide biosynthetic process
P	0016787	molecular_function	hydrolase activity
P	0016788	molecular_function	hydrolase activity, acting on ester bonds
P	0019143	molecular_function	3-deoxy-manno-octulosonate-8-phosphatase activity
P	0046872	molecular_function	metal ion binding

Functional Information from PDB Data

site_id	AC1
Number of Residues	6
Details	BINDING SITE FOR RESIDUE CA A 201

Chain	Residue
A	ASP32
A	ASP34
A	ASP125
A	PO4202
A	HOH203
A	HOH204

site_id	AC2
Number of Residues	6
Details	BINDING SITE FOR RESIDUE CA B 202

Chain	Residue
B	ASP125
B	PO4203
B	HOH205
A	HOH302
B	ASP32
B	ASP34

site_id	AC3
Number of Residues	6
Details	BINDING SITE FOR RESIDUE CA C 203

Chain	Residue
C	ASP32
C	ASP34
C	ASP125
C	PO4204
C	HOH205
C	HOH206

site_id	AC4
Number of Residues	6
Details	BINDING SITE FOR RESIDUE CA D 204

Chain	Residue
C	HOH207
D	ASP32
D	ASP34
D	ASP125
D	PO4205
D	HOH209

site_id	AC5
Number of Residues	6
Details	BINDING SITE FOR RESIDUE CA E 205

Chain	Residue
E	ASP32
E	ASP34
E	ASP125
E	PO4206
E	HOH208
H	HOH210

site_id	AC6
Number of Residues	6
Details	BINDING SITE FOR RESIDUE CA F 206

Chain	Residue
F	ASP32
F	ASP34
F	ASP125
F	PO4207
F	HOH238
F	HOH252

site_id	AC7
Number of Residues	6
Details	BINDING SITE FOR RESIDUE CA G 207

Chain	Residue
G	ASP32
G	ASP34
G	ASP125
G	PO4208
G	HOH210
G	HOH400

site_id	AC8
Number of Residues	6
Details	BINDING SITE FOR RESIDUE CA H 208

Chain	Residue
G	HOH212
H	ASP32
H	ASP34
H	ASP125
H	PO4209
H	HOH211

site_id	AC9
Number of Residues	6
Details	BINDING SITE FOR RESIDUE CA I 209

Chain	Residue
I	ASP32
I	ASP34
I	ASP125
I	PO4210
I	HOH211
I	HOH270

site_id	BC1
Number of Residues	5
Details	BINDING SITE FOR RESIDUE CA J 210

Chain	Residue
J	ASP32
J	ASP34
J	ASP125
J	PO4211
J	HOH309

site_id	BC2
Number of Residues	5
Details	BINDING SITE FOR RESIDUE CA K 211

Chain	Residue
K	ASP32
K	ASP34
K	ASP125
K	PO4212
K	HOH213

site_id	BC3
Number of Residues	5
Details	BINDING SITE FOR RESIDUE CA L 212

Chain	Residue
L	ASP32
L	ASP34
L	ASP125
L	PO4213
L	HOH215

site_id	BC4
Number of Residues	6
Details	BINDING SITE FOR RESIDUE CA M 213

Chain	Residue
M	ASP32
M	ASP34
M	ASP125
M	PO4214
M	HOH277
M	HOH329

site_id	BC5
Number of Residues	6
Details	BINDING SITE FOR RESIDUE CA N 214

Chain	Residue
M	HOH221
N	ASP32
N	ASP34
N	ASP125
N	PO4215
N	HOH217

site_id	BC6
Number of Residues	6
Details	BINDING SITE FOR RESIDUE CA O 215

Chain	Residue
O	ASP32
O	ASP34
O	ASP125
O	PO4216
O	HOH221
O	HOH222

site_id	BC7
Number of Residues	6
Details	BINDING SITE FOR RESIDUE CA P 216

Chain	Residue
P	ASP32
P	ASP34
P	ASP125
P	PO4217
P	HOH218
P	HOH299

site_id	BC8
Number of Residues	11
Details	BINDING SITE FOR RESIDUE PO4 A 202

Chain	Residue
A	CA201
A	HOH203
A	HOH204
A	HOH205
D	SER187
A	ASP32
A	VAL33
A	ASP34
A	THR76
A	GLY77
A	LYS102

site_id	BC9
Number of Residues	9
Details	BINDING SITE FOR RESIDUE PO4 B 203

Chain	Residue
A	SER187
B	ASP32
B	VAL33
B	ASP34
B	THR76
B	GLY77
B	LYS102
B	CA202
B	HOH206

site_id	CC1
Number of Residues	11
Details	BINDING SITE FOR RESIDUE PO4 C 204

Chain	Residue
B	SER187
B	HOH207
C	ASP32
C	VAL33
C	ASP34
C	THR76
C	GLY77
C	LYS102
C	CA203
C	HOH205
C	HOH206

site_id	CC2
Number of Residues	10
Details	BINDING SITE FOR RESIDUE PO4 D 205

Chain	Residue
C	SER187
D	ASP32
D	VAL33
D	ASP34
D	THR76
D	GLY77
D	LYS102
D	CA204
D	HOH209
D	HOH210

site_id	CC3
Number of Residues	10
Details	BINDING SITE FOR RESIDUE PO4 E 206

Chain	Residue
E	ASP32
E	VAL33
E	ASP34
E	THR76
E	GLY77
E	LYS102
E	CA205
E	HOH208
E	HOH209
H	SER187

site_id	CC4
Number of Residues	9
Details	BINDING SITE FOR RESIDUE PO4 F 207

Chain	Residue
F	ASP32
F	VAL33
F	ASP34
F	THR76
F	GLY77
F	LYS102
F	CA206
F	HOH238
F	HOH374

site_id	CC5
Number of Residues	12
Details	BINDING SITE FOR RESIDUE PO4 G 208

Chain	Residue
F	SER187
G	ASP32
G	VAL33
G	ASP34
G	THR76
G	GLY77
G	ARG78
G	LYS102
G	CA207
G	HOH210
G	HOH211
G	HOH400

site_id	CC6
Number of Residues	9
Details	BINDING SITE FOR RESIDUE PO4 H 209

Chain	Residue
G	SER187
H	ASP32
H	VAL33
H	ASP34
H	THR76
H	GLY77
H	LYS102
H	CA208
H	HOH212

site_id	CC7
Number of Residues	10
Details	BINDING SITE FOR RESIDUE PO4 I 210

Chain	Residue
I	ASP32
I	VAL33
I	ASP34
I	THR76
I	GLY77
I	ARG78
I	LYS102
I	CA209
I	HOH270
L	SER187

site_id	CC8
Number of Residues	10
Details	BINDING SITE FOR RESIDUE PO4 J 211

Chain	Residue
I	SER187
J	ASP32
J	VAL33
J	ASP34
J	THR76
J	GLY77
J	ARG78
J	LYS102
J	CA210
J	HOH212

site_id	CC9
Number of Residues	10
Details	BINDING SITE FOR RESIDUE PO4 K 212

Chain	Residue
J	SER187
K	ASP32
K	VAL33
K	ASP34
K	THR76
K	GLY77
K	ARG78
K	LYS102
K	CA211
K	HOH294

site_id	DC1
Number of Residues	9
Details	BINDING SITE FOR RESIDUE PO4 L 213

Chain	Residue
K	SER187
L	ASP32
L	VAL33
L	ASP34
L	THR76
L	GLY77
L	LYS102
L	CA212
L	HOH214

site_id	DC2
Number of Residues	9
Details	BINDING SITE FOR RESIDUE PO4 M 214

Chain	Residue
M	ASP32
M	VAL33
M	ASP34
M	THR76
M	GLY77
M	ARG78
M	LYS102
M	CA213
M	HOH329

site_id	DC3
Number of Residues	11
Details	BINDING SITE FOR RESIDUE PO4 N 215

Chain	Residue
M	SER187
M	HOH221
N	ASP32
N	VAL33
N	ASP34
N	THR76
N	GLY77
N	ARG78
N	LYS102
N	CA214
N	HOH218

site_id	DC4
Number of Residues	10
Details	BINDING SITE FOR RESIDUE PO4 O 216

Chain	Residue
O	ASP32
O	VAL33
O	ASP34
O	THR76
O	GLY77
O	ARG78
O	LYS102
O	CA215
O	HOH221
O	HOH223

site_id	DC5
Number of Residues	10
Details	BINDING SITE FOR RESIDUE PO4 P 217

Chain	Residue
P	ASP32
P	VAL33
P	ASP34
P	THR76
P	GLY77
P	ARG78
P	LYS102
P	CA216
P	HOH299
P	HOH329

Functional Information from SwissProt/UniProt

site_id	SWS_FT_FI1
Number of Residues	176
Details	Binding site: {"evidences":[{"source":"PubMed","id":"19726684","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

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