5BPF

Crystal structure of ADP complexed D-alanine-D-alanine ligase(DDL) from Yersinia pestis

Functional Information from GO Data

Chain	GOid	namespace	contents
A	0003824	molecular_function	catalytic activity
A	0005524	molecular_function	ATP binding
A	0005737	cellular_component	cytoplasm
A	0005829	cellular_component	cytosol
A	0008360	biological_process	regulation of cell shape
A	0008716	molecular_function	D-alanine-D-alanine ligase activity
A	0009252	biological_process	peptidoglycan biosynthetic process
A	0016874	molecular_function	ligase activity
A	0046872	molecular_function	metal ion binding
A	0071555	biological_process	cell wall organization
B	0003824	molecular_function	catalytic activity
B	0005524	molecular_function	ATP binding
B	0005737	cellular_component	cytoplasm
B	0005829	cellular_component	cytosol
B	0008360	biological_process	regulation of cell shape
B	0008716	molecular_function	D-alanine-D-alanine ligase activity
B	0009252	biological_process	peptidoglycan biosynthetic process
B	0016874	molecular_function	ligase activity
B	0046872	molecular_function	metal ion binding
B	0071555	biological_process	cell wall organization
C	0003824	molecular_function	catalytic activity
C	0005524	molecular_function	ATP binding
C	0005737	cellular_component	cytoplasm
C	0005829	cellular_component	cytosol
C	0008360	biological_process	regulation of cell shape
C	0008716	molecular_function	D-alanine-D-alanine ligase activity
C	0009252	biological_process	peptidoglycan biosynthetic process
C	0016874	molecular_function	ligase activity
C	0046872	molecular_function	metal ion binding
C	0071555	biological_process	cell wall organization
D	0003824	molecular_function	catalytic activity
D	0005524	molecular_function	ATP binding
D	0005737	cellular_component	cytoplasm
D	0005829	cellular_component	cytosol
D	0008360	biological_process	regulation of cell shape
D	0008716	molecular_function	D-alanine-D-alanine ligase activity
D	0009252	biological_process	peptidoglycan biosynthetic process
D	0016874	molecular_function	ligase activity
D	0046872	molecular_function	metal ion binding
D	0071555	biological_process	cell wall organization

Functional Information from PDB Data

site_id	AC1
Number of Residues	6
Details	binding site for residue NA A 401

Chain	Residue
A	GLU68
A	SER91
A	THR94
A	MET95
A	THR273
A	HOH551

---

site_id	AC2
Number of Residues	2
Details	binding site for residue GOL A 402

Chain	Residue
A	TYR223
A	HOH512

---

site_id	AC3
Number of Residues	6
Details	binding site for residue GOL A 403

Chain	Residue
A	PRO82
A	TYR83
A	GLY85
A	GLY87
A	ASP306
A	GLU77

---

site_id	AC4
Number of Residues	2
Details	binding site for residue NA A 404

Chain	Residue
A	HIS265
C	HIS280

---

site_id	AC5
Number of Residues	13
Details	binding site for residue ADP B 401

Chain	Residue
B	LYS97
B	SER112
B	LYS144
B	SER151
B	MET154
B	GLU180
B	LYS181
B	TRP182
B	LEU183
B	GLU187
B	TYR210
B	MET259
B	GLU270

---

site_id	AC6
Number of Residues	6
Details	binding site for residue NA B 402

Chain	Residue
B	GLU68
B	SER91
B	THR94
B	MET95
B	THR273
B	HOH546

---

site_id	AC7
Number of Residues	4
Details	binding site for residue ACT B 403

Chain	Residue
B	GLY11
B	THR12
B	THR42
B	GLY66

---

site_id	AC8
Number of Residues	5
Details	binding site for residue ACT B 404

Chain	Residue
B	TYR83
B	GLY85
B	GLY87
B	HOH512
B	HOH526

---

site_id	AC9
Number of Residues	15
Details	binding site for residue ADP C 401

Chain	Residue
C	LYS97
C	ILE142
C	LYS144
C	GLU148
C	SER151
C	GLU180
C	LYS181
C	LEU183
C	GLU187
C	PHE209
C	TYR210
C	LYS215
C	MET259
C	GLU270
C	HOH586

---

site_id	AD1
Number of Residues	6
Details	binding site for residue NA C 402

Chain	Residue
C	GLU68
C	SER91
C	THR94
C	MET95
C	THR273
C	HOH591

---

site_id	AD2
Number of Residues	6
Details	binding site for residue ACT C 403

Chain	Residue
C	GLY276
C	SER281
C	LEU282
C	HOH501
C	HOH508
C	HOH515

---

site_id	AD3
Number of Residues	4
Details	binding site for residue ACT C 404

Chain	Residue
C	GLN80
C	ASP306
C	HOH541
C	HOH575

---

site_id	AD4
Number of Residues	5
Details	binding site for residue GOL C 405

Chain	Residue
C	PRO82
C	TYR83
C	GLY85
C	ASP306
C	HOH549

---

site_id	AD5
Number of Residues	15
Details	binding site for residue ADP D 401

Chain	Residue
D	LYS97
D	ILE142
D	LYS144
D	SER151
D	MET154
D	GLU180
D	LYS181
D	TRP182
D	LEU183
D	GLU187
D	PHE209
D	TYR210
D	MET259
D	GLU270
D	HOH538

---

site_id	AD6
Number of Residues	6
Details	binding site for residue NA D 402

Chain	Residue
D	THR273
D	HOH546
D	GLU68
D	SER91
D	THR94
D	MET95

---

site_id	AD7
Number of Residues	7
Details	binding site for residue GOL D 403

Chain	Residue
D	LEU76
D	GLU77
D	LEU81
D	PRO82
D	TYR83
D	ASP306
D	HOH519

---

site_id	AD8
Number of Residues	8
Details	binding site for residue GOL D 404

Chain	Residue
D	PRO82
D	TYR83
D	GLY85
D	SER86
D	GLY87
D	SER251
D	ASP306
D	HOH503

---

Functional Information from PROSITE/UniProt

site_id	PS00843
Number of Residues	12
Details	DALA_DALA_LIGASE_1 D-alanine--D-alanine ligase signature 1. HGrgGEDGtLQG

Chain	Residue	Details
A	HIS63-GLY74

---

site_id	PS00844
Number of Residues	29
Details	DALA_DALA_LIGASE_2 D-alanine--D-alanine ligase signature 2. LdcsGwGRVDVMqdrdghfy....LlEVNTsPG

Chain	Residue	Details
A	LEU248-GLY276

---

Functional Information from SwissProt/UniProt

site_id	SWS_FT_FI1
Number of Residues	16
Details	BINDING: BINDING => ECO:0000255|HAMAP-Rule:MF_00047

Chain	Residue	Details
B	VAL134
B	ASP257
B	GLU270
B	ASN272
C	VAL134
C	ASP257
C	GLU270
C	ASN272
D	VAL134
D	ASP257
D	GLU270
D	ASN272
A	VAL134
A	ASP257
A	GLU270
A	ASN272

---