Summary Structural details Experimental details Functional details Sequence Neighbor History Downloads

5ZQD

Crystal Structure of Penicillin-Binding Protein D2 from Listeria monocytogenes in the Cefotaxime bound form

Functional Information from GO Data

Chain	GOid	namespace	contents
A	0006508	biological_process	proteolysis
A	0009002	molecular_function	serine-type D-Ala-D-Ala carboxypeptidase activity
B	0006508	biological_process	proteolysis
B	0009002	molecular_function	serine-type D-Ala-D-Ala carboxypeptidase activity
C	0006508	biological_process	proteolysis
C	0009002	molecular_function	serine-type D-Ala-D-Ala carboxypeptidase activity
D	0006508	biological_process	proteolysis
D	0009002	molecular_function	serine-type D-Ala-D-Ala carboxypeptidase activity
E	0006508	biological_process	proteolysis
E	0009002	molecular_function	serine-type D-Ala-D-Ala carboxypeptidase activity
F	0006508	biological_process	proteolysis
F	0009002	molecular_function	serine-type D-Ala-D-Ala carboxypeptidase activity
G	0006508	biological_process	proteolysis
G	0009002	molecular_function	serine-type D-Ala-D-Ala carboxypeptidase activity
H	0006508	biological_process	proteolysis
H	0009002	molecular_function	serine-type D-Ala-D-Ala carboxypeptidase activity

Functional Information from PDB Data

site_id	AC1
Number of Residues	11
Details	binding site for residue CEF A 301

Chain	Residue
A	ALA57
A	ARG257
A	HOH485
A	SER58
A	VAL94
A	SER118
A	ASN120
A	THR223
A	GLY224
A	PHE225
A	THR226

site_id	AC2
Number of Residues	10
Details	binding site for residue GOL A 302

Chain	Residue
A	LEU69
A	VAL72
A	ASP73
A	TRP79
A	GLU187
A	HOH427
A	HOH467
D	TYR28
D	SER30
D	LYS256

site_id	AC3
Number of Residues	8
Details	binding site for residue GOL B 302

Chain	Residue
B	VAL72
B	ASP73
B	TRP79
B	GLU187
B	HOH437
C	TYR28
C	SER30
C	LYS256

site_id	AC4
Number of Residues	5
Details	binding site for residue GOL B 303

Chain	Residue
B	GLY164
B	SER166
B	GLU228
B	HOH486
F	GLY213

site_id	AC5
Number of Residues	3
Details	binding site for residue GOL B 304

Chain	Residue
B	GLY42
B	LYS172
B	PHE175

site_id	AC6
Number of Residues	9
Details	binding site for residue GOL C 302

Chain	Residue
B	TYR28
B	LEU29
B	SER30
B	LYS256
C	LEU69
C	ASP73
C	TRP79
C	GLU187
C	HOH457

site_id	AC7
Number of Residues	9
Details	binding site for residue GOL D 302

Chain	Residue
A	TYR28
A	SER30
A	LYS256
D	VAL72
D	ASP73
D	TRP79
D	GLU187
D	HOH461
D	HOH482

site_id	AC8
Number of Residues	7
Details	binding site for residue GOL E 302

Chain	Residue
E	VAL72
E	ASP73
E	TRP79
E	GLU187
E	HOH427
H	SER30
H	LYS256

site_id	AC9
Number of Residues	3
Details	binding site for residue GOL E 303

Chain	Residue
E	SER30
E	ASP250
E	ALA251

site_id	AD1
Number of Residues	7
Details	binding site for residue GOL F 302

Chain	Residue
F	VAL72
F	ASP73
F	TRP79
F	GLU187
F	HOH484
G	SER30
G	LYS256

site_id	AD2
Number of Residues	9
Details	binding site for residue GOL G 302

Chain	Residue
F	TYR28
F	SER30
F	LYS256
G	LEU69
G	VAL72
G	ASP73
G	TRP79
G	GLU187
G	HOH416

site_id	AD3
Number of Residues	9
Details	binding site for residue GOL H 302

Chain	Residue
E	TYR28
E	LEU29
E	HOH419
H	LEU69
H	VAL72
H	ASP73
H	TRP79
H	GLU187
H	HOH472

site_id	AD4
Number of Residues	15
Details	binding site for Di-peptide CEF B 301 and SER B 58

Chain	Residue
B	LEU160
B	THR223
B	GLY224
B	PHE225
B	THR226
B	ARG257
B	ILE56
B	ALA57
B	LEU59
B	SER60
B	LYS61
B	VAL94
B	SER118
B	ASN120
B	SER158

site_id	AD5
Number of Residues	16
Details	binding site for Di-peptide CEF C 301 and SER C 58

Chain	Residue
C	ILE56
C	ALA57
C	LEU59
C	SER60
C	LYS61
C	SER118
C	ASN120
C	SER158
C	LEU160
C	LYS222
C	THR223
C	GLY224
C	PHE225
C	THR226
C	ARG257
C	HOH405

site_id	AD6
Number of Residues	16
Details	binding site for Di-peptide CEF C 303 and LYS C 204

Chain	Residue
A	LYS82
A	LEU83
A	ASP84
A	THR104
A	HOH409
C	VAL197
C	THR198
C	GLY202
C	ALA203
C	LEU205
C	HOH401
C	HOH412
C	HOH422
C	HOH483
C	HOH488
C	HOH502

site_id	AD7
Number of Residues	20
Details	binding site for Di-peptide CEF D 301 and SER D 58

Chain	Residue
D	ILE56
D	ALA57
D	LEU59
D	SER60
D	LYS61
D	VAL94
D	SER118
D	ASN120
D	SER158
D	LEU160
D	THR208
D	LYS222
D	THR223
D	GLY224
D	PHE225
D	THR226
D	ARG257
D	HOH401
D	HOH444
D	HOH491

site_id	AD8
Number of Residues	13
Details	binding site for Di-peptide CEF D 303 and LYS D 204

Chain	Residue
B	LYS82
B	LEU83
B	ASP84
B	THR104
B	HOH406
B	HOH422
D	VAL197
D	GLY202
D	ALA203
D	LEU205
D	HOH405
D	HOH438
D	HOH450

site_id	AD9
Number of Residues	17
Details	binding site for Di-peptide CEF E 301 and SER E 58

Chain	Residue
E	ILE56
E	ALA57
E	LEU59
E	SER60
E	LYS61
E	VAL94
E	SER118
E	ASN120
E	SER158
E	LEU160
E	THR208
E	THR223
E	GLY224
E	PHE225
E	THR226
E	ARG257
E	HOH405

site_id	AE1
Number of Residues	17
Details	binding site for Di-peptide CEF F 301 and SER F 58

Chain	Residue
F	ILE56
F	ALA57
F	LEU59
F	SER60
F	LYS61
F	VAL94
F	SER118
F	ASN120
F	SER158
F	LEU160
F	LYS222
F	THR223
F	GLY224
F	PHE225
F	THR226
F	ARG257
F	HOH454

site_id	AE2
Number of Residues	18
Details	binding site for Di-peptide CEF G 301 and SER G 58

Chain	Residue
G	ILE56
G	ALA57
G	LEU59
G	SER60
G	LYS61
G	VAL94
G	SER118
G	ASN120
G	SER158
G	LEU160
G	LYS222
G	THR223
G	GLY224
G	PHE225
G	THR226
G	ARG257
G	HOH458
G	HOH498

site_id	AE3
Number of Residues	8
Details	binding site for Di-peptide CEF G 303 and LYS G 204

Chain	Residue
G	VAL197
G	GLY202
G	ALA203
G	LEU205
G	GLU206
G	HOH401
G	HOH403
G	HOH470

site_id	AE4
Number of Residues	16
Details	binding site for Di-peptide CEF H 301 and SER H 58

Chain	Residue
H	ILE56
H	ALA57
H	LEU59
H	SER60
H	LYS61
H	VAL94
H	SER118
H	ASN120
H	SER158
H	THR208
H	THR223
H	GLY224
H	PHE225
H	THR226
H	ARG257
H	HOH491

site_id	AE5
Number of Residues	8
Details	binding site for Di-peptide CEF H 303 and LYS H 204

Chain	Residue
H	VAL197
H	GLY202
H	ALA203
H	LEU205
H	GLU206
H	HOH438
H	HOH446
H	HOH520

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