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3VMM

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

Functional Information from GO Data
ChainGOidnamespacecontents
A0003824molecular_functioncatalytic activity
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 Residues2
DetailsBINDING: BINDING => ECO:0000269|PubMed:22407814
ChainResidueDetails
AGLU109
ALEU182

site_idSWS_FT_FI2
Number of Residues9
DetailsBINDING: BINDING => ECO:0000269|PubMed:22407814, ECO:0000269|PubMed:24702628
ChainResidueDetails
ALYS138
ALYS178
ASER184
AGLU226
AGLN268
AHIS309
AGLU311
AGLU324
AARG328

site_idSWS_FT_FI3
Number of Residues1
DetailsBINDING: BINDING => ECO:0000269|PubMed:24702628
ChainResidueDetails
AGLU273

site_idSWS_FT_FI4
Number of Residues1
DetailsSITE: Plays a key role in restricting the N-terminal substrate specificity to small amino acids such as L-Ala => ECO:0000269|PubMed:24702628
ChainResidueDetails
ATRP332

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PDB entries from 2024-10-09

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