Summary Structural details Experimental details Functional details Sequence Neighbor History Downloads

6U1K

Thermus thermophilus D-alanine-D-alanine ligase in complex with ADP, carbonate, D-alanine-D-alanine, Mg2+ and K+

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	7
Details	binding site for residue MG A 403

Chain	Residue
A	GLU282
A	ASN284
A	MG404
A	K405
A	ADP406
A	CO3407
A	HOH616

site_id	AC2
Number of Residues	6
Details	binding site for residue MG A 404

Chain	Residue
A	ADP406
A	CO3407
A	HOH513
A	HOH583
A	GLU282
A	MG403

site_id	AC3
Number of Residues	8
Details	binding site for residue K A 405

Chain	Residue
A	CYS113
A	GLU282
A	LEU283
A	ASN284
A	MG403
A	HOH608
A	HOH616
A	HOH622

site_id	AC4
Number of Residues	28
Details	binding site for residue ADP A 406

Chain	Residue
A	LYS116
A	PHE151
A	LYS153
A	THR157
A	GLY158
A	SER159
A	SER160
A	ILE163
A	GLU189
A	LYS190
A	ALA191
A	LEU192
A	GLU197
A	TYR218
A	PHE222
A	TYR223
A	LYS228
A	PHE272
A	ASN281
A	GLU282
A	MG403
A	MG404
A	CO3407
A	HOH513
A	HOH555
A	HOH583
A	HOH596
A	HOH616

site_id	AC5
Number of Residues	13
Details	binding site for residue CO3 A 407

Chain	Residue
A	SER159
A	LYS228
A	ARG268
A	GLU282
A	ASN284
A	DAL401
A	DAL402
A	MG403
A	MG404
A	ADP406
A	HOH513
A	HOH583
A	HOH595

site_id	AC6
Number of Residues	6
Details	binding site for residue MG B 403

Chain	Residue
B	GLU282
B	MG404
B	ADP406
B	CO3407
B	HOH508
B	HOH592

site_id	AC7
Number of Residues	7
Details	binding site for residue MG B 404

Chain	Residue
B	GLU282
B	ASN284
B	MG403
B	K405
B	ADP406
B	CO3407
B	HOH567

site_id	AC8
Number of Residues	8
Details	binding site for residue K B 405

Chain	Residue
B	CYS113
B	GLU282
B	LEU283
B	ASN284
B	MG404
B	HOH512
B	HOH567
B	HOH619

site_id	AC9
Number of Residues	27
Details	binding site for residue ADP B 406

Chain	Residue
B	PHE272
B	ASN281
B	GLU282
B	MG403
B	MG404
B	CO3407
B	HOH508
B	HOH559
B	HOH567
B	HOH592
B	HOH596
B	LYS116
B	PHE151
B	LYS153
B	THR157
B	GLY158
B	SER159
B	SER160
B	ILE163
B	GLU189
B	LYS190
B	ALA191
B	LEU192
B	GLU197
B	PHE222
B	TYR223
B	LYS228

site_id	AD1
Number of Residues	13
Details	binding site for residue CO3 B 407

Chain	Residue
B	SER159
B	LYS228
B	ARG268
B	GLU282
B	ASN284
B	DAL401
B	DAL402
B	MG403
B	MG404
B	ADP406
B	HOH508
B	HOH535
B	HOH592

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

Chain	Residue
C	GLU282
C	MG404
C	ADP406
C	CO3407
C	HOH525
C	HOH585

site_id	AD3
Number of Residues	7
Details	binding site for residue MG C 404

Chain	Residue
C	GLU282
C	ASN284
C	MG403
C	K405
C	ADP406
C	CO3407
C	HOH558

site_id	AD4
Number of Residues	8
Details	binding site for residue K C 405

Chain	Residue
C	CYS113
C	GLU282
C	LEU283
C	ASN284
C	MG404
C	HOH537
C	HOH558
C	HOH604

site_id	AD5
Number of Residues	26
Details	binding site for residue ADP C 406

Chain	Residue
C	LYS116
C	PHE151
C	LYS153
C	THR157
C	GLY158
C	SER159
C	SER160
C	ILE163
C	GLU189
C	LYS190
C	LEU192
C	GLU197
C	TYR218
C	PHE222
C	TYR223
C	LYS228
C	PHE272
C	ASN281
C	GLU282
C	MG403
C	MG404
C	CO3407
C	HOH558
C	HOH574
C	HOH585
C	HOH634

site_id	AD6
Number of Residues	12
Details	binding site for residue CO3 C 407

Chain	Residue
C	SER159
C	LYS228
C	ARG268
C	GLU282
C	ASN284
C	DAL401
C	DAL402
C	MG403
C	MG404
C	ADP406
C	HOH547
C	HOH585

site_id	AD7
Number of Residues	6
Details	binding site for residue MG D 403

Chain	Residue
D	GLU282
D	MG404
D	ADP406
D	CO3407
D	HOH512
D	HOH588

site_id	AD8
Number of Residues	7
Details	binding site for residue MG D 404

Chain	Residue
D	GLU282
D	ASN284
D	MG403
D	K405
D	ADP406
D	CO3407
D	HOH567

site_id	AD9
Number of Residues	8
Details	binding site for residue K D 405

Chain	Residue
D	CYS113
D	GLU282
D	LEU283
D	ASN284
D	MG404
D	HOH523
D	HOH567
D	HOH587

site_id	AE1
Number of Residues	27
Details	binding site for residue ADP D 406

Chain	Residue
D	LYS116
D	PHE151
D	LYS153
D	THR157
D	GLY158
D	SER159
D	SER160
D	ILE163
D	GLU189
D	LYS190
D	ALA191
D	LEU192
D	GLU197
D	TYR218
D	PHE222
D	TYR223
D	LYS228
D	PHE272
D	ASN281
D	GLU282
D	MG403
D	MG404
D	CO3407
D	HOH512
D	HOH577
D	HOH588
D	HOH622

site_id	AE2
Number of Residues	12
Details	binding site for residue CO3 D 407

Chain	Residue
D	SER159
D	LYS228
D	ARG268
D	GLU282
D	ASN284
D	DAL401
D	DAL402
D	MG403
D	MG404
D	ADP406
D	HOH548
D	HOH588

site_id	AE3
Number of Residues	12
Details	binding site for Di-peptide DAL A 401 and DAL A 402

Chain	Residue
A	GLU13
A	HIS82
A	SER159
A	TYR229
A	ARG268
A	GLY288
A	SER293
A	MET294
A	CO3407
A	HOH525
A	HOH528
A	HOH612

site_id	AE4
Number of Residues	14
Details	binding site for Di-peptide DAL B 401 and DAL B 402

Chain	Residue
B	GLU13
B	HIS82
B	SER159
B	TYR223
B	TYR229
B	ARG268
B	GLY288
B	SER293
B	MET294
B	CO3407
B	HOH547
B	HOH555
B	HOH582
B	HOH591

site_id	AE5
Number of Residues	13
Details	binding site for Di-peptide DAL C 401 and DAL C 402

Chain	Residue
C	GLU13
C	HIS82
C	SER159
C	LYS228
C	TYR229
C	ARG268
C	GLY288
C	SER293
C	MET294
C	CO3407
C	HOH550
C	HOH553
C	HOH577

site_id	AE6
Number of Residues	13
Details	binding site for Di-peptide DAL D 401 and DAL D 402

Chain	Residue
D	GLU13
D	HIS82
D	SER159
D	TYR229
D	ARG268
D	GLY288
D	SER293
D	MET294
D	CO3407
D	HOH559
D	HOH564
D	HOH576
D	HOH613

Functional Information from PROSITE/UniProt

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

Chain	Residue	Details
A	HIS82-GLY93

site_id	PS00844
Number of Residues	28
Details	DALA_DALA_LIGASE_2 D-alanine--D-alanine ligase signature 2. LgvrGmARVDFFlaegely.....LnELNTiPG

Chain	Residue	Details
A	LEU261-GLY288

Functional Information from SwissProt/UniProt

site_id	SWS_FT_FI1
Number of Residues	585
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	216
Details	Binding site: {"evidences":[{"source":"HAMAP-Rule","id":"MF_00047","evidenceCode":"ECO:0000255"}]}

Chain

Residue

Details

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