Summary Structural details Experimental details Functional details Sequence Neighbor History Downloads

3T88

Crystal structure of Escherichia coli MenB in complex with substrate analogue, OSB-NCoA

Functional Information from GO Data

Chain	GOid	namespace	contents
A	0003824	molecular_function	catalytic activity
A	0005515	molecular_function	protein binding
A	0005829	cellular_component	cytosol
A	0008935	molecular_function	1,4-dihydroxy-2-naphthoyl-CoA synthase activity
A	0009234	biological_process	menaquinone biosynthetic process
A	0016829	molecular_function	lyase activity
A	0071890	molecular_function	bicarbonate binding
B	0003824	molecular_function	catalytic activity
B	0005515	molecular_function	protein binding
B	0005829	cellular_component	cytosol
B	0008935	molecular_function	1,4-dihydroxy-2-naphthoyl-CoA synthase activity
B	0009234	biological_process	menaquinone biosynthetic process
B	0016829	molecular_function	lyase activity
B	0071890	molecular_function	bicarbonate binding
C	0003824	molecular_function	catalytic activity
C	0005515	molecular_function	protein binding
C	0005829	cellular_component	cytosol
C	0008935	molecular_function	1,4-dihydroxy-2-naphthoyl-CoA synthase activity
C	0009234	biological_process	menaquinone biosynthetic process
C	0016829	molecular_function	lyase activity
C	0071890	molecular_function	bicarbonate binding
D	0003824	molecular_function	catalytic activity
D	0005515	molecular_function	protein binding
D	0005829	cellular_component	cytosol
D	0008935	molecular_function	1,4-dihydroxy-2-naphthoyl-CoA synthase activity
D	0009234	biological_process	menaquinone biosynthetic process
D	0016829	molecular_function	lyase activity
D	0071890	molecular_function	bicarbonate binding
E	0003824	molecular_function	catalytic activity
E	0005515	molecular_function	protein binding
E	0005829	cellular_component	cytosol
E	0008935	molecular_function	1,4-dihydroxy-2-naphthoyl-CoA synthase activity
E	0009234	biological_process	menaquinone biosynthetic process
E	0016829	molecular_function	lyase activity
E	0071890	molecular_function	bicarbonate binding
F	0003824	molecular_function	catalytic activity
F	0005515	molecular_function	protein binding
F	0005829	cellular_component	cytosol
F	0008935	molecular_function	1,4-dihydroxy-2-naphthoyl-CoA synthase activity
F	0009234	biological_process	menaquinone biosynthetic process
F	0016829	molecular_function	lyase activity
F	0071890	molecular_function	bicarbonate binding

Functional Information from PDB Data

site_id	AC1
Number of Residues	29
Details	BINDING SITE FOR RESIDUE S0N A 300

Chain	Residue
A	GLN43
A	GLN88
A	LYS89
A	TYR97
A	LEU106
A	VAL108
A	LEU109
A	TYR129
A	ILE131
A	GLY133
A	THR155
A	VAL44
A	VAL159
A	SER161
A	PHE162
A	ASP163
A	GLN189
A	HOH1190
A	HOH1196
E	TYR258
E	PHE270
E	LYS273
A	ARG45
A	ALA47
A	PHE48
A	SER84
A	GLY85
A	GLY86
A	ASP87

site_id	AC2
Number of Residues	6
Details	BINDING SITE FOR RESIDUE CL A 301

Chain	Residue
A	GLY132
A	GLN154
A	THR155
A	GLY156
A	TRP184
A	HOH1190

site_id	AC3
Number of Residues	3
Details	BINDING SITE FOR RESIDUE PGE A 302

Chain	Residue
A	LYS54
A	HIS105
E	TYR65

site_id	AC4
Number of Residues	5
Details	BINDING SITE FOR RESIDUE GOL A 303

Chain	Residue
A	THR203
A	GLU213
A	ARG216
A	TRP217
C	ARG188

site_id	AC5
Number of Residues	30
Details	BINDING SITE FOR RESIDUE S0N B 400

Chain	Residue
B	GLN43
B	VAL44
B	ARG45
B	ALA47
B	PHE48
B	SER84
B	GLY85
B	GLY86
B	ASP87
B	GLN88
B	LYS89
B	TYR97
B	VAL108
B	LEU109
B	TYR129
B	ILE131
B	GLY133
B	THR155
B	VAL159
B	SER161
B	PHE162
B	ASP163
B	GLN189
B	HOH326
B	HOH513
B	HOH1191
D	LYS280
F	TYR258
F	PHE270
F	LYS273

site_id	AC6
Number of Residues	6
Details	BINDING SITE FOR RESIDUE CL B 401

Chain	Residue
B	GLY132
B	GLN154
B	THR155
B	GLY156
B	TRP184
B	HOH1191

site_id	AC7
Number of Residues	3
Details	BINDING SITE FOR RESIDUE PGE B 402

Chain	Residue
B	LYS54
B	HIS105
F	TYR65

site_id	AC8
Number of Residues	6
Details	BINDING SITE FOR RESIDUE GOL B 403

Chain	Residue
A	ARG188
B	THR203
B	VAL205
B	GLU213
B	ARG216
B	TRP217

site_id	AC9
Number of Residues	28
Details	BINDING SITE FOR RESIDUE S0N C 500

Chain	Residue
C	VAL108
C	LEU109
C	TYR129
C	ILE131
C	GLY133
C	THR155
C	VAL159
C	SER161
C	PHE162
C	GLN189
C	HOH288
C	HOH505
C	HOH648
C	HOH1192
D	TYR258
D	PHE270
D	LYS273
C	GLN43
C	VAL44
C	ARG45
C	ALA47
C	SER84
C	GLY85
C	GLY86
C	ASP87
C	GLN88
C	LYS89
C	TYR97

site_id	BC1
Number of Residues	6
Details	BINDING SITE FOR RESIDUE CL C 501

Chain	Residue
C	GLY132
C	GLN154
C	THR155
C	GLY156
C	TRP184
C	HOH1192

site_id	BC2
Number of Residues	4
Details	BINDING SITE FOR RESIDUE PGE C 502

Chain	Residue
C	LYS54
C	HIS105
C	HOH311
C	HOH1131

site_id	BC3
Number of Residues	6
Details	BINDING SITE FOR RESIDUE GOL C 503

Chain	Residue
B	ARG188
C	THR203
C	VAL205
C	GLU213
C	ARG216
C	TRP217

site_id	BC4
Number of Residues	29
Details	BINDING SITE FOR RESIDUE S0N D 600

Chain	Residue
C	TYR258
C	PHE270
D	GLN43
D	VAL44
D	ARG45
D	ALA47
D	PHE48
D	SER84
D	GLY85
D	GLY86
D	ASP87
D	GLN88
D	LYS89
D	TYR97
D	VAL108
D	LEU109
D	TYR129
D	ILE131
D	GLY132
D	GLY133
D	THR155
D	VAL159
D	SER161
D	PHE162
D	ASP163
D	GLN189
D	HOH766
D	HOH914
D	HOH1193

site_id	BC5
Number of Residues	6
Details	BINDING SITE FOR RESIDUE CL D 601

Chain	Residue
D	GLY132
D	GLN154
D	THR155
D	GLY156
D	TRP184
D	HOH1193

site_id	BC6
Number of Residues	4
Details	BINDING SITE FOR RESIDUE PGE D 602

Chain	Residue
C	TYR65
D	LYS54
D	HIS105
D	ASN107

site_id	BC7
Number of Residues	7
Details	BINDING SITE FOR RESIDUE GOL D 603

Chain	Residue
D	THR203
D	VAL205
D	GLU213
D	ARG216
D	TRP217
D	HOH683
E	ARG188

site_id	BC8
Number of Residues	30
Details	BINDING SITE FOR RESIDUE S0N E 700

Chain	Residue
A	TYR258
A	PHE270
A	LYS273
E	GLN43
E	VAL44
E	ARG45
E	ALA47
E	PHE48
E	SER84
E	GLY85
E	GLY86
E	ASP87
E	GLN88
E	LYS89
E	TYR97
E	LEU106
E	VAL108
E	LEU109
E	TYR129
E	ILE131
E	GLY133
E	THR155
E	VAL159
E	SER161
E	PHE162
E	ASP163
E	GLN189
E	HOH321
E	HOH473
E	HOH1194

site_id	BC9
Number of Residues	6
Details	BINDING SITE FOR RESIDUE CL E 701

Chain	Residue
E	GLY132
E	GLN154
E	THR155
E	GLY156
E	TRP184
E	HOH1194

site_id	CC1
Number of Residues	4
Details	BINDING SITE FOR RESIDUE PGE E 702

Chain	Residue
E	LYS54
E	HIS105
E	HOH312
E	HOH1208

site_id	CC2
Number of Residues	6
Details	BINDING SITE FOR RESIDUE GOL E 703

Chain	Residue
E	THR203
E	VAL205
E	GLU213
E	ARG216
E	TRP217
F	ARG188

site_id	CC3
Number of Residues	27
Details	BINDING SITE FOR RESIDUE S0N F 800

Chain	Residue
B	TYR258
B	PHE270
B	LYS273
F	GLN43
F	VAL44
F	ARG45
F	ALA47
F	PHE48
F	SER84
F	GLY85
F	GLY86
F	ASP87
F	GLN88
F	LYS89
F	TYR97
F	VAL108
F	LEU109
F	TYR129
F	ILE131
F	GLY133
F	THR155
F	VAL159
F	SER161
F	PHE162
F	ASP163
F	GLN189
F	HOH1195

site_id	CC4
Number of Residues	6
Details	BINDING SITE FOR RESIDUE CL F 801

Chain	Residue
F	GLY132
F	GLN154
F	THR155
F	GLY156
F	TRP184
F	HOH1195

site_id	CC5
Number of Residues	2
Details	BINDING SITE FOR RESIDUE PGE F 802

Chain	Residue
F	LYS54
F	HIS105

site_id	CC6
Number of Residues	6
Details	BINDING SITE FOR RESIDUE GOL F 803

Chain	Residue
D	ARG188
F	THR203
F	VAL205
F	GLU213
F	ARG216
F	TRP217

Functional Information from PROSITE/UniProt

site_id	PS00166
Number of Residues	21
Details	ENOYL_COA_HYDRATASE Enoyl-CoA hydratase/isomerase signature. VAmVAGysiGGGhvlhMmCDL

Chain	Residue	Details
A	VAL123-LEU143

Functional Information from SwissProt/UniProt

site_id	SWS_FT_FI1
Number of Residues	36
Details	Binding site: {"description":"in other chain","evidences":[{"source":"HAMAP-Rule","id":"MF_01934","evidenceCode":"ECO:0000255"},{"source":"PubMed","id":"21830810","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"23658663","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

site_id	SWS_FT_FI2
Number of Residues	30
Details	Binding site: {"description":"in other chain","evidences":[{"source":"PubMed","id":"21830810","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"23658663","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

site_id	SWS_FT_FI3
Number of Residues	6
Details	Binding site: {"description":"in other chain","evidences":[{"source":"HAMAP-Rule","id":"MF_01934","evidenceCode":"ECO:0000255"},{"source":"PubMed","id":"21830810","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

site_id	SWS_FT_FI4
Number of Residues	12
Details	Binding site: {"evidences":[{"source":"HAMAP-Rule","id":"MF_01934","evidenceCode":"ECO:0000255"},{"source":"PubMed","id":"22606952","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

site_id	SWS_FT_FI5
Number of Residues	6
Details	Binding site: {"description":"in other chain","evidences":[{"source":"HAMAP-Rule","id":"MF_01934","evidenceCode":"ECO:0000255"},{"source":"PubMed","id":"23658663","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

site_id	SWS_FT_FI6
Number of Residues	6
Details	Binding site: {"evidences":[{"source":"HAMAP-Rule","id":"MF_01934","evidenceCode":"ECO:0000255"},{"source":"PubMed","id":"21830810","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

site_id	SWS_FT_FI7
Number of Residues	6
Details	Binding site: {"evidences":[{"source":"HAMAP-Rule","id":"MF_01934","evidenceCode":"ECO:0000255"},{"source":"PubMed","id":"21830810","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"23658663","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

site_id	SWS_FT_FI8
Number of Residues	12
Details	Site: {"description":"Important for catalysis","evidences":[{"source":"HAMAP-Rule","id":"MF_01934","evidenceCode":"ECO:0000255"},{"source":"PubMed","id":"21830810","evidenceCode":"ECO:0000305"}]}

Chain

Residue

Details

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