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3VMM

Crystal structure of BacD, an L-amino acid dipeptide ligase from Bacillus subtilis

Functional Information from GO Data
ChainGOidnamespacecontents
A0000166molecular_functionnucleotide binding
A0005524molecular_functionATP binding
A0016874molecular_functionligase activity
A0017000biological_processantibiotic biosynthetic process
A0034026molecular_functionL-amino-acid alpha-ligase activity
A0046872molecular_functionmetal ion binding
Functional Information from PDB Data
site_idAC1
Number of Residues5
DetailsBINDING SITE FOR RESIDUE MG A 501
ChainResidue
AGLU311
AGLU324
AADP503
AP0D504
AHOH719

site_idAC2
Number of Residues8
DetailsBINDING SITE FOR RESIDUE MG A 502
ChainResidue
AGLU324
AADP503
AP0D504
AHOH721
AGLU109
ALYS138
ALEU182
AALA183

site_idAC3
Number of Residues24
DetailsBINDING SITE FOR RESIDUE ADP A 503
ChainResidue
ALYS138
AILE176
ALYS178
ALEU182
AALA183
ASER184
ASER185
AVAL188
AGLU226
AGLU227
APHE228
ALEU229
AGLN268
APHE271
AGLU311
AILE323
AGLU324
AMG501
AMG502
AP0D504
AHOH631
AHOH685
AHOH706
AHOH719

site_idAC4
Number of Residues19
DetailsBINDING SITE FOR RESIDUE P0D A 504
ChainResidue
ALEU12
AGLY13
AGLY14
AALA183
ASER184
AGLU273
AHIS309
AGLU311
AGLU324
AARG328
AGLY331
AMG501
AMG502
AADP503
AHOH650
AHOH719
AHOH721
AHOH744
AHOH745

Functional Information from SwissProt/UniProt
site_idSWS_FT_FI1
Number of Residues213
DetailsDomain: {"description":"ATP-grasp","evidences":[{"source":"PROSITE-ProRule","id":"PRU00409","evidenceCode":"ECO:0000255"}]}
ChainResidueDetails

site_idSWS_FT_FI2
Number of Residues2
DetailsBinding site: {"evidences":[{"source":"PubMed","id":"22407814","evidenceCode":"ECO:0000269"}]}
ChainResidueDetails

site_idSWS_FT_FI3
Number of Residues14
DetailsBinding site: {"evidences":[{"source":"PubMed","id":"22407814","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"24702628","evidenceCode":"ECO:0000269"}]}
ChainResidueDetails

site_idSWS_FT_FI4
Number of Residues1
DetailsBinding site: {"evidences":[{"source":"PubMed","id":"24702628","evidenceCode":"ECO:0000269"}]}
ChainResidueDetails

site_idSWS_FT_FI5
Number of Residues1
DetailsSite: {"description":"Plays a key role in restricting the N-terminal substrate specificity to small amino acids such as L-Ala","evidences":[{"source":"PubMed","id":"24702628","evidenceCode":"ECO:0000269"}]}
ChainResidueDetails

243911

PDB entries from 2025-10-29

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