Summary Structural details Experimental details Functional details Sequence Neighbor History Downloads

4A1I

ykud from B.subtilis

Functional Information from GO Data

Chain	GOid	namespace	contents
A	0008360	biological_process	regulation of cell shape
A	0009252	biological_process	peptidoglycan biosynthetic process
A	0016740	molecular_function	transferase activity
A	0016757	molecular_function	glycosyltransferase activity
A	0016787	molecular_function	hydrolase activity
A	0018104	biological_process	peptidoglycan-protein cross-linking
A	0030435	biological_process	sporulation resulting in formation of a cellular spore
A	0031160	cellular_component	spore wall
A	0071555	biological_process	cell wall organization
A	0071972	molecular_function	peptidoglycan L,D-transpeptidase activity
B	0008360	biological_process	regulation of cell shape
B	0009252	biological_process	peptidoglycan biosynthetic process
B	0016740	molecular_function	transferase activity
B	0016757	molecular_function	glycosyltransferase activity
B	0016787	molecular_function	hydrolase activity
B	0018104	biological_process	peptidoglycan-protein cross-linking
B	0030435	biological_process	sporulation resulting in formation of a cellular spore
B	0031160	cellular_component	spore wall
B	0071555	biological_process	cell wall organization
B	0071972	molecular_function	peptidoglycan L,D-transpeptidase activity
C	0008360	biological_process	regulation of cell shape
C	0009252	biological_process	peptidoglycan biosynthetic process
C	0016740	molecular_function	transferase activity
C	0016757	molecular_function	glycosyltransferase activity
C	0016787	molecular_function	hydrolase activity
C	0018104	biological_process	peptidoglycan-protein cross-linking
C	0030435	biological_process	sporulation resulting in formation of a cellular spore
C	0031160	cellular_component	spore wall
C	0071555	biological_process	cell wall organization
C	0071972	molecular_function	peptidoglycan L,D-transpeptidase activity
D	0008360	biological_process	regulation of cell shape
D	0009252	biological_process	peptidoglycan biosynthetic process
D	0016740	molecular_function	transferase activity
D	0016757	molecular_function	glycosyltransferase activity
D	0016787	molecular_function	hydrolase activity
D	0018104	biological_process	peptidoglycan-protein cross-linking
D	0030435	biological_process	sporulation resulting in formation of a cellular spore
D	0031160	cellular_component	spore wall
D	0071555	biological_process	cell wall organization
D	0071972	molecular_function	peptidoglycan L,D-transpeptidase activity
E	0008360	biological_process	regulation of cell shape
E	0009252	biological_process	peptidoglycan biosynthetic process
E	0016740	molecular_function	transferase activity
E	0016757	molecular_function	glycosyltransferase activity
E	0016787	molecular_function	hydrolase activity
E	0018104	biological_process	peptidoglycan-protein cross-linking
E	0030435	biological_process	sporulation resulting in formation of a cellular spore
E	0031160	cellular_component	spore wall
E	0071555	biological_process	cell wall organization
E	0071972	molecular_function	peptidoglycan L,D-transpeptidase activity
F	0008360	biological_process	regulation of cell shape
F	0009252	biological_process	peptidoglycan biosynthetic process
F	0016740	molecular_function	transferase activity
F	0016757	molecular_function	glycosyltransferase activity
F	0016787	molecular_function	hydrolase activity
F	0018104	biological_process	peptidoglycan-protein cross-linking
F	0030435	biological_process	sporulation resulting in formation of a cellular spore
F	0031160	cellular_component	spore wall
F	0071555	biological_process	cell wall organization
F	0071972	molecular_function	peptidoglycan L,D-transpeptidase activity
G	0008360	biological_process	regulation of cell shape
G	0009252	biological_process	peptidoglycan biosynthetic process
G	0016740	molecular_function	transferase activity
G	0016757	molecular_function	glycosyltransferase activity
G	0016787	molecular_function	hydrolase activity
G	0018104	biological_process	peptidoglycan-protein cross-linking
G	0030435	biological_process	sporulation resulting in formation of a cellular spore
G	0031160	cellular_component	spore wall
G	0071555	biological_process	cell wall organization
G	0071972	molecular_function	peptidoglycan L,D-transpeptidase activity
H	0008360	biological_process	regulation of cell shape
H	0009252	biological_process	peptidoglycan biosynthetic process
H	0016740	molecular_function	transferase activity
H	0016757	molecular_function	glycosyltransferase activity
H	0016787	molecular_function	hydrolase activity
H	0018104	biological_process	peptidoglycan-protein cross-linking
H	0030435	biological_process	sporulation resulting in formation of a cellular spore
H	0031160	cellular_component	spore wall
H	0071555	biological_process	cell wall organization
H	0071972	molecular_function	peptidoglycan L,D-transpeptidase activity

Functional Information from PDB Data

site_id	AC1
Number of Residues	10
Details	BINDING SITE FOR RESIDUE SO4 A 1165

Chain	Residue
A	HIS123
H	HIS119
A	SER136
A	LYS137
A	GLY138
A	CYS139
A	ARG141
A	CD1169
A	CL1170
A	HOH2184

site_id	AC2
Number of Residues	9
Details	BINDING SITE FOR RESIDUE SO4 A 1166

Chain	Residue
A	THR92
A	ARG164
A	HOH2157
A	HOH2220
A	HOH2221
A	HOH2222
A	HOH2223
D	LEU12
H	ASN13

site_id	AC3
Number of Residues	5
Details	BINDING SITE FOR RESIDUE SO4 A 1167

Chain	Residue
A	ASN127
A	VAL135
A	ARG141
A	HOH2190
A	HOH2202

site_id	AC4
Number of Residues	9
Details	BINDING SITE FOR RESIDUE SO4 A 1168

Chain	Residue
A	LEU12
A	HOH2048
A	HOH2049
A	HOH2051
A	HOH2224
A	HOH2225
D	THR92
D	ARG164
E	HOH2032

site_id	AC5
Number of Residues	5
Details	BINDING SITE FOR RESIDUE CD A 1169

Chain	Residue
A	CYS139
A	SO41165
A	CL1170
A	HOH2184
H	HIS119

site_id	AC6
Number of Residues	6
Details	BINDING SITE FOR RESIDUE CL A 1170

Chain	Residue
A	PHE108
A	HIS119
A	SO41165
A	CD1169
A	HOH2184
H	HIS119

site_id	AC7
Number of Residues	9
Details	BINDING SITE FOR RESIDUE SO4 B 1165

Chain	Residue
B	HIS123
B	SER136
B	LYS137
B	GLY138
B	CYS139
B	ARG141
B	CD1167
B	CL1168
B	HOH2170

site_id	AC8
Number of Residues	6
Details	BINDING SITE FOR RESIDUE SO4 B 1166

Chain	Residue
B	THR92
B	ARG164
B	HOH2202
B	HOH2203
B	HOH2204
B	HOH2205

site_id	AC9
Number of Residues	4
Details	BINDING SITE FOR RESIDUE CD B 1167

Chain	Residue
B	CYS139
B	SO41165
B	CL1168
B	HOH2170

site_id	BC1
Number of Residues	5
Details	BINDING SITE FOR RESIDUE CL B 1168

Chain	Residue
B	PHE108
B	HIS119
B	SO41165
B	CD1167
B	HOH2170

site_id	BC2
Number of Residues	11
Details	BINDING SITE FOR RESIDUE SO4 C 1165

Chain	Residue
C	HIS123
C	SER136
C	LYS137
C	GLY138
C	CYS139
C	ARG141
C	CD1168
C	CL1169
C	HOH2173
C	HOH2200
F	HIS119

site_id	BC3
Number of Residues	7
Details	BINDING SITE FOR RESIDUE SO4 C 1166

Chain	Residue
C	THR92
C	ARG164
C	HOH2149
C	HOH2199
C	HOH2201
C	HOH2202
C	HOH2203

site_id	BC4
Number of Residues	5
Details	BINDING SITE FOR RESIDUE SO4 C 1167

Chain	Residue
C	ASN127
C	VAL135
C	ARG141
C	HOH2184
C	HOH2187

site_id	BC5
Number of Residues	5
Details	BINDING SITE FOR RESIDUE CD C 1168

Chain	Residue
C	CYS139
C	SO41165
C	CL1169
C	HOH2173
F	HIS119

site_id	BC6
Number of Residues	7
Details	BINDING SITE FOR RESIDUE CL C 1169

Chain	Residue
C	CD1168
C	HOH2173
F	HIS119
F	HOH2128
C	PHE108
C	HIS119
C	SO41165

site_id	BC7
Number of Residues	11
Details	BINDING SITE FOR RESIDUE SO4 D 1165

Chain	Residue
D	HIS123
D	SER136
D	LYS137
D	GLY138
D	CYS139
D	ARG141
D	CD1166
D	CL1167
D	HOH2175
D	HOH2211
E	HIS119

site_id	BC8
Number of Residues	5
Details	BINDING SITE FOR RESIDUE CD D 1166

Chain	Residue
D	CYS139
D	SO41165
D	CL1167
D	HOH2175
E	HIS119

site_id	BC9
Number of Residues	7
Details	BINDING SITE FOR RESIDUE CL D 1167

Chain	Residue
D	PHE108
D	TRP112
D	HIS119
D	SO41165
D	CD1166
D	HOH2175
E	HIS119

site_id	CC1
Number of Residues	11
Details	BINDING SITE FOR RESIDUE SO4 E 1165

Chain	Residue
D	HIS119
E	HIS123
E	SER136
E	LYS137
E	GLY138
E	CYS139
E	ARG141
E	CD1168
E	CL1169
E	HOH2144
E	HOH2169

site_id	CC2
Number of Residues	7
Details	BINDING SITE FOR RESIDUE SO4 E 1166

Chain	Residue
A	ASN73
A	ARG159
A	HOH2121
E	GLU94
E	TYR96
E	ARG159
E	HOH2006

site_id	CC3
Number of Residues	3
Details	BINDING SITE FOR RESIDUE SO4 E 1167

Chain	Residue
E	ASN127
E	ARG141
E	HOH2147

site_id	CC4
Number of Residues	5
Details	BINDING SITE FOR RESIDUE CD E 1168

Chain	Residue
D	HIS119
E	CYS139
E	SO41165
E	CL1169
E	HOH2144

site_id	CC5
Number of Residues	8
Details	BINDING SITE FOR RESIDUE CL E 1169

Chain	Residue
D	HIS119
E	PHE108
E	TRP112
E	HIS119
E	SO41165
E	CD1168
E	HOH2115
E	HOH2144

site_id	CC6
Number of Residues	11
Details	BINDING SITE FOR RESIDUE SO4 F 1165

Chain	Residue
C	HIS119
F	HIS123
F	SER136
F	LYS137
F	GLY138
F	CYS139
F	ARG141
F	CD1168
F	CL1169
F	HOH2162
F	HOH2192

site_id	CC7
Number of Residues	5
Details	BINDING SITE FOR RESIDUE SO4 F 1166

Chain	Residue
F	TYR96
F	ARG159
F	HOH2005
F	HOH2101
F	HOH2194

site_id	CC8
Number of Residues	4
Details	BINDING SITE FOR RESIDUE SO4 F 1167

Chain	Residue
F	ASN127
F	ARG141
F	HOH2163
F	HOH2173

site_id	CC9
Number of Residues	5
Details	BINDING SITE FOR RESIDUE CD F 1168

Chain	Residue
C	HIS119
F	CYS139
F	SO41165
F	CL1169
F	HOH2162

site_id	DC1
Number of Residues	8
Details	BINDING SITE FOR RESIDUE CL F 1169

Chain	Residue
C	HIS119
F	PHE108
F	TRP112
F	HIS119
F	SO41165
F	CD1168
F	HOH2128
F	HOH2162

site_id	DC2
Number of Residues	11
Details	BINDING SITE FOR RESIDUE SO4 G 1165

Chain	Residue
G	HIS123
G	SER136
G	LYS137
G	GLY138
G	CYS139
G	ARG141
G	CD1168
G	CL1169
G	HOH2133
G	HOH2160
G	HOH2161

site_id	DC3
Number of Residues	4
Details	BINDING SITE FOR RESIDUE SO4 G 1166

Chain	Residue
C	ARG159
G	TYR96
G	ARG159
G	HOH2005

site_id	DC4
Number of Residues	3
Details	BINDING SITE FOR RESIDUE SO4 G 1167

Chain	Residue
G	ASN127
G	ARG141
G	HOH2136

site_id	DC5
Number of Residues	4
Details	BINDING SITE FOR RESIDUE CD G 1168

Chain	Residue
G	CYS139
G	SO41165
G	CL1169
G	HOH2133

site_id	DC6
Number of Residues	7
Details	BINDING SITE FOR RESIDUE CL G 1169

Chain	Residue
G	PHE108
G	TRP112
G	HIS119
G	SO41165
G	CD1168
G	HOH2102
G	HOH2133

site_id	DC7
Number of Residues	11
Details	BINDING SITE FOR RESIDUE SO4 H 1165

Chain	Residue
A	HIS119
H	HIS123
H	SER136
H	LYS137
H	GLY138
H	CYS139
H	ARG141
H	CD1168
H	CL1169
H	HOH2136
H	HOH2166

site_id	DC8
Number of Residues	8
Details	BINDING SITE FOR RESIDUE SO4 H 1166

Chain	Residue
D	ASN73
D	ARG159
D	HOH2114
H	TYR96
H	ARG159
H	HOH2004
H	HOH2112
H	HOH2167

site_id	DC9
Number of Residues	4
Details	BINDING SITE FOR RESIDUE SO4 H 1167

Chain	Residue
H	ASN127
H	ARG141
H	HOH2139
H	HOH2168

site_id	EC1
Number of Residues	5
Details	BINDING SITE FOR RESIDUE CD H 1168

Chain	Residue
A	HIS119
H	CYS139
H	SO41165
H	CL1169
H	HOH2136

site_id	EC2
Number of Residues	8
Details	BINDING SITE FOR RESIDUE CL H 1169

Chain	Residue
A	HIS119
A	LYS137
H	PHE108
H	TRP112
H	HIS119
H	SO41165
H	CD1168
H	HOH2136

Functional Information from SwissProt/UniProt

site_id	SWS_FT_FI1
Number of Residues	344
Details	Domain: {"description":"LysM","evidences":[{"source":"PROSITE-ProRule","id":"PRU01118","evidenceCode":"ECO:0000255"}]}

Chain

Residue

Details

site_id	SWS_FT_FI2
Number of Residues	856
Details	Domain: {"description":"L,D-TPase catalytic","evidences":[{"source":"PROSITE-ProRule","id":"PRU01373","evidenceCode":"ECO:0000255"}]}

Chain

Residue

Details

site_id	SWS_FT_FI3
Number of Residues	8
Details	Active site: {"description":"Proton donor/acceptor","evidences":[{"source":"PROSITE-ProRule","id":"PRU01373","evidenceCode":"ECO:0000255"}]}

Chain

Residue

Details

site_id	SWS_FT_FI4
Number of Residues	8
Details	Active site: {"description":"Nucleophile","evidences":[{"source":"PROSITE-ProRule","id":"PRU01373","evidenceCode":"ECO:0000255"}]}

Chain

Residue

Details

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