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2ZDQ

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

Functional Information from GO Data
ChainGOidnamespacecontents
A0000166molecular_functionnucleotide binding
A0005524molecular_functionATP binding
A0005737cellular_componentcytoplasm
A0005829cellular_componentcytosol
A0008360biological_processregulation of cell shape
A0008716molecular_functionD-alanine-D-alanine ligase activity
A0009252biological_processpeptidoglycan biosynthetic process
A0016874molecular_functionligase activity
A0046872molecular_functionmetal ion binding
A0071555biological_processcell wall organization
B0000166molecular_functionnucleotide binding
B0005524molecular_functionATP binding
B0005737cellular_componentcytoplasm
B0005829cellular_componentcytosol
B0008360biological_processregulation of cell shape
B0008716molecular_functionD-alanine-D-alanine ligase activity
B0009252biological_processpeptidoglycan biosynthetic process
B0016874molecular_functionligase activity
B0046872molecular_functionmetal ion binding
B0071555biological_processcell wall organization
Functional Information from PDB Data
site_idAC1
Number of Residues5
DetailsBINDING SITE FOR RESIDUE DAL A 401
ChainResidue
AGLU13
ATYR229
AARG268
AASN284
AGLY288

site_idAC2
Number of Residues7
DetailsBINDING SITE FOR RESIDUE DAL A 402
ChainResidue
AMET294
AHOH1508
AHOH1509
ATYR229
AARG268
AGLY288
ASER293

site_idAC3
Number of Residues4
DetailsBINDING SITE FOR RESIDUE DAL B 403
ChainResidue
BGLU13
BTYR229
BARG268
BGLY288

site_idAC4
Number of Residues6
DetailsBINDING SITE FOR RESIDUE DAL B 404
ChainResidue
BLYS228
BTYR229
BARG268
BSER293
BMET294
BHOH1546

site_idAC5
Number of Residues26
DetailsBINDING SITE FOR RESIDUE ATP A 1501
ChainResidue
ALYS116
APHE151
ALYS153
AGLY158
ASER159
ASER160
AILE163
AGLU189
ALYS190
AALA191
ALEU192
AGLU197
ATYR218
APHE222
ATYR223
ALYS228
AARG268
AASP270
APHE272
AASN281
AGLU282
AASN284
AHOH1502
AHOH1530
AHOH1536
AHOH1579

site_idAC6
Number of Residues24
DetailsBINDING SITE FOR RESIDUE ATP B 1502
ChainResidue
BLYS116
BPHE151
BLYS153
BGLY158
BSER159
BSER160
BILE163
BGLU189
BLYS190
BALA191
BLEU192
BGLU197
BTYR218
BPHE222
BTYR223
BLYS228
BARG268
BASP270
BPHE272
BASN281
BGLU282
BASN284
BHOH1504
BHOH1547

Functional Information from PROSITE/UniProt
site_idPS00843
Number of Residues12
DetailsDALA_DALA_LIGASE_1 D-alanine--D-alanine ligase signature 1. HGrfGEDGtVQG
ChainResidueDetails
AHIS82-GLY93

site_idPS00844
Number of Residues28
DetailsDALA_DALA_LIGASE_2 D-alanine--D-alanine ligase signature 2. LgvrGmARVDFFlaegely.....LnELNTiPG
ChainResidueDetails
ALEU261-GLY288

Functional Information from SwissProt/UniProt
site_idSWS_FT_FI1
Number of Residues390
DetailsDomain: {"description":"ATP-grasp","evidences":[{"source":"HAMAP-Rule","id":"MF_00047","evidenceCode":"ECO:0000255"}]}
ChainResidueDetails

site_idSWS_FT_FI2
Number of Residues108
DetailsBinding site: {"evidences":[{"source":"HAMAP-Rule","id":"MF_00047","evidenceCode":"ECO:0000255"}]}
ChainResidueDetails

Catalytic Information from CSA
site_idCSA1
Number of Residues5
DetailsAnnotated By Reference To The Literature 2dln
ChainResidueDetails
AGLU13
ATYR229
AARG268
AGLY288
ASER159

site_idCSA2
Number of Residues5
DetailsAnnotated By Reference To The Literature 2dln
ChainResidueDetails
BGLU13
BTYR229
BARG268
BGLY288
BSER159

249697

PDB entries from 2026-02-25

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