5BPH

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

Functional Information from GO Data

Chain	GOid	namespace	contents
A	0000166	molecular_function	nucleotide binding
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	0000166	molecular_function	nucleotide binding
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	0000166	molecular_function	nucleotide binding
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	0000166	molecular_function	nucleotide binding
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	16
Details	binding site for residue AMP A 401

Chain	Residue
A	LYS97
A	PHE209
A	TYR210
A	MET259
A	GLU270
A	HOH524
A	HOH598
A	HOH601
A	ILE142
A	LYS144
A	MET154
A	GLU180
A	LYS181
A	TRP182
A	LEU183
A	GLU187

---

site_id	AC2
Number of Residues	6
Details	binding site for residue NA A 402

Chain	Residue
A	GLU68
A	SER91
A	THR94
A	MET95
A	THR273
A	HOH575

---

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

Chain	Residue
A	GLY276
A	SER281
A	LEU282
A	HOH508
A	HOH560
A	HOH566

---

site_id	AC4
Number of Residues	5
Details	binding site for residue GOL A 404

Chain	Residue
A	LEU76
A	GLU77
A	GLN80
A	LEU81
A	ASP306

---

site_id	AC5
Number of Residues	6
Details	binding site for residue GOL A 405

Chain	Residue
A	LEU107
A	HIS246
A	ALA247
A	HOH502
D	ALA116
D	ASN118

---

site_id	AC6
Number of Residues	2
Details	binding site for residue NA A 406

Chain	Residue
A	HIS280
B	HIS265

---

site_id	AC7
Number of Residues	19
Details	binding site for residue AMP B 401

Chain	Residue
B	LYS97
B	ILE142
B	LYS144
B	MET154
B	GLU180
B	LYS181
B	TRP182
B	LEU183
B	GLU187
B	VAL208
B	PHE209
B	TYR210
B	MET259
B	GLU270
B	HOH514
B	HOH516
B	HOH527
B	HOH531
B	HOH537

---

site_id	AC8
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	HOH566

---

site_id	AC9
Number of Residues	8
Details	binding site for residue ACT B 403

Chain	Residue
B	LYS215
B	TYR216
B	ARG255
B	ASN272
B	PRO275
B	GLY276
B	ACT404
B	HOH572

---

site_id	AD1
Number of Residues	7
Details	binding site for residue ACT B 404

Chain	Residue
B	LYS215
B	TYR216
B	GLY276
B	SER281
B	LEU282
B	ACT403
B	HOH555

---

site_id	AD2
Number of Residues	5
Details	binding site for residue GOL B 405

Chain	Residue
B	GLY11
B	THR12
B	THR42
B	GLY66
B	HOH618

---

site_id	AD3
Number of Residues	15
Details	binding site for residue AMP C 401

Chain	Residue
C	HOH518
C	HOH542
C	LYS97
C	ILE142
C	LYS144
C	GLU180
C	LYS181
C	TRP182
C	LEU183
C	GLU187
C	PHE209
C	TYR210
C	MET259
C	GLU270
C	HOH503

---

site_id	AD4
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	HOH551

---

site_id	AD5
Number of Residues	7
Details	binding site for residue ACT C 403

Chain	Residue
C	TYR210
C	GLY276
C	SER281
C	LEU282
C	HOH501
C	HOH514
C	HOH533

---

site_id	AD6
Number of Residues	7
Details	binding site for residue GOL C 404

Chain	Residue
C	PRO82
C	TYR83
C	GLY85
C	SER86
C	GLY87
C	SER251
C	ASP306

---

site_id	AD7
Number of Residues	7
Details	binding site for residue GOL C 405

Chain	Residue
C	GLY11
C	THR12
C	THR42
C	ARG65
C	GLY66
C	HOH531
C	HOH534

---

site_id	AD8
Number of Residues	16
Details	binding site for residue AMP D 401

Chain	Residue
D	LYS97
D	ILE142
D	LYS144
D	GLU180
D	LYS181
D	TRP182
D	LEU183
D	GLU187
D	PHE209
D	TYR210
D	MET259
D	LEU269
D	GLU270
D	HOH538
D	HOH576
D	HOH584

---

site_id	AD9
Number of Residues	6
Details	binding site for residue NA D 402

Chain	Residue
D	GLU68
D	SER91
D	THR94
D	MET95
D	THR273
D	HOH558

---

site_id	AE1
Number of Residues	6
Details	binding site for residue ACT D 403

Chain	Residue
D	ARG255
D	GLY276
D	SER281
D	LEU282
D	ACT406
D	HOH548

---

site_id	AE2
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	HOH506

---

site_id	AE3
Number of Residues	6
Details	binding site for residue GOL D 405

Chain	Residue
D	LEU76
D	GLU77
D	GLN80
D	LEU81
D	ASP306
D	HOH516

---

site_id	AE4
Number of Residues	6
Details	binding site for residue ACT D 406

Chain	Residue
D	LYS215
D	ARG255
D	ASN272
D	GLY276
D	ACT403
D	HOH518

---

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	606
Details	Domain: {"description":"ATP-grasp","evidences":[{"source":"HAMAP-Rule","id":"MF_00047","evidenceCode":"ECO:0000255"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI2
Number of Residues	177
Details	Binding site: {"evidences":[{"source":"HAMAP-Rule","id":"MF_00047","evidenceCode":"ECO:0000255"}]}

Chain

Residue

Details

---