Summary Structural details Experimental details Functional details Sequence Neighbor History Downloads

2ZDH

Crystal structure of D-Alanine:D-Alanine Ligase with ADP and D-Alanine from Thermus thermophius HB8

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	2
Details	BINDING SITE FOR RESIDUE MG A 811

Chain	Residue
A	GLU282
A	ASN284

site_id	AC2
Number of Residues	2
Details	BINDING SITE FOR RESIDUE MG A 812

Chain	Residue
A	ASP270
A	GLU282

site_id	AC3
Number of Residues	1
Details	BINDING SITE FOR RESIDUE MG B 813

Chain	Residue
B	GLU282

site_id	AC4
Number of Residues	1
Details	BINDING SITE FOR RESIDUE MG B 814

Chain	Residue
B	GLU282

site_id	AC5
Number of Residues	1
Details	BINDING SITE FOR RESIDUE MG C 815

Chain	Residue
C	GLU282

site_id	AC6
Number of Residues	1
Details	BINDING SITE FOR RESIDUE MG C 816

Chain	Residue
C	GLU282

site_id	AC7
Number of Residues	2
Details	BINDING SITE FOR RESIDUE MG D 817

Chain	Residue
D	GLU282
D	ASP270

site_id	AC8
Number of Residues	19
Details	BINDING SITE FOR RESIDUE ADP A 701

Chain	Residue
A	LYS116
A	PHE151
A	LYS153
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

site_id	AC9
Number of Residues	15
Details	BINDING SITE FOR RESIDUE ADP B 702

Chain	Residue
B	LYS116
B	PHE151
B	LYS153
B	SER159
B	SER160
B	ILE163
B	GLU189
B	LYS190
B	ALA191
B	LEU192
B	GLU197
B	PHE272
B	ASN281
B	GLU282
C	ALA220

site_id	BC1
Number of Residues	6
Details	BINDING SITE FOR RESIDUE DAL A 801

Chain	Residue
A	GLU13
A	HIS82
A	TYR229
A	ARG268
A	ASN284
A	GLY288

site_id	BC2
Number of Residues	16
Details	BINDING SITE FOR RESIDUE ADP C 703

Chain	Residue
B	ALA220
C	LYS116
C	PHE151
C	LYS153
C	GLY158
C	SER159
C	SER160
C	ILE163
C	GLU189
C	LYS190
C	ALA191
C	LEU192
C	GLU197
C	PHE272
C	ASN281
C	GLU282

site_id	BC3
Number of Residues	17
Details	BINDING SITE FOR RESIDUE ADP D 704

Chain	Residue
D	LYS116
D	PHE151
D	LYS153
D	GLY158
D	SER159
D	SER160
D	ILE163
D	GLU189
D	LYS190
D	LEU192
D	GLU197
D	TYR218
D	PHE222
D	TYR223
D	PHE272
D	ASN281
D	GLU282

site_id	BC4
Number of Residues	5
Details	BINDING SITE FOR RESIDUE DAL D 802

Chain	Residue
D	GLU13
D	HIS82
D	ARG268
D	ASN284
D	GLY288

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	16
Details	BINDING: BINDING => ECO:0000255\|HAMAP-Rule:MF_00047

Chain	Residue	Details
A	ASP147
C	ASP270
C	GLU282
C	ASN284
D	ASP147
D	ASP270
D	GLU282
D	ASN284
A	ASP270
A	GLU282
A	ASN284
B	ASP147
B	ASP270
B	GLU282
B	ASN284
C	ASP147

Catalytic Information from CSA

site_id	CSA1
Number of Residues	5
Details	Annotated By Reference To The Literature 2dln

Chain	Residue	Details
A	GLU13
A	TYR229
A	ARG268
A	GLY288
A	SER159

site_id	CSA2
Number of Residues	4
Details	Annotated By Reference To The Literature 2dln

Chain	Residue	Details
B	GLU13
B	ARG268
B	GLY288
B	SER159

site_id	CSA3
Number of Residues	5
Details	Annotated By Reference To The Literature 2dln

Chain	Residue	Details
C	GLU13
C	TYR229
C	ARG268
C	GLY288
C	SER159

site_id	CSA4
Number of Residues	5
Details	Annotated By Reference To The Literature 2dln

Chain	Residue	Details
D	GLU13
D	TYR229
D	ARG268
D	GLY288
D	SER159

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