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3WO0

Crystal structure of Bacillus subtilis YwfE, an L-amino acid ligase, with bound ADP-Mg-Ala

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 Residues22
DetailsBINDING SITE FOR RESIDUE ADP A 501
ChainResidue
ALYS138
ALEU229
AGLN268
APHE271
AGLU311
AGLU324
AMG502
AMG503
AHOH1001
AHOH1029
AHOH1032
ALYS178
AHOH1033
AHOH1181
AHOH1200
AALA183
ASER184
ASER185
AVAL188
AGLU226
AGLU227
APHE228

site_idAC2
Number of Residues6
DetailsBINDING SITE FOR RESIDUE MG A 502
ChainResidue
AGLU311
AGLU324
AADP501
AMG503
AHOH1001
AHOH1032

site_idAC3
Number of Residues7
DetailsBINDING SITE FOR RESIDUE MG A 503
ChainResidue
ALYS138
AGLU324
AADP501
AMG502
AHOH1029
AHOH1030
AHOH1200

site_idAC4
Number of Residues9
DetailsBINDING SITE FOR RESIDUE ALA A 504
ChainResidue
AGLU273
AHIS309
AGLU311
AARG328
AGLY331
AMET334
AHOH1001
AHOH1003
AHOH1202

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

246704

PDB entries from 2025-12-24

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