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4B4Z

Crystal structure of a complex between Actinomadura R39 DD-peptidase and a sulfonamide boronate inhibitor

Functional Information from GO Data
ChainGOidnamespacecontents
A0000270biological_processpeptidoglycan metabolic process
A0004180molecular_functioncarboxypeptidase activity
A0004185molecular_functionserine-type carboxypeptidase activity
A0005576cellular_componentextracellular region
A0006508biological_processproteolysis
A0008233molecular_functionpeptidase activity
A0008360biological_processregulation of cell shape
A0009002molecular_functionserine-type D-Ala-D-Ala carboxypeptidase activity
A0009252biological_processpeptidoglycan biosynthetic process
A0016787molecular_functionhydrolase activity
A0046677biological_processresponse to antibiotic
A0071555biological_processcell wall organization
B0000270biological_processpeptidoglycan metabolic process
B0004180molecular_functioncarboxypeptidase activity
B0004185molecular_functionserine-type carboxypeptidase activity
B0005576cellular_componentextracellular region
B0006508biological_processproteolysis
B0008233molecular_functionpeptidase activity
B0008360biological_processregulation of cell shape
B0009002molecular_functionserine-type D-Ala-D-Ala carboxypeptidase activity
B0009252biological_processpeptidoglycan biosynthetic process
B0016787molecular_functionhydrolase activity
B0046677biological_processresponse to antibiotic
B0071555biological_processcell wall organization
C0000270biological_processpeptidoglycan metabolic process
C0004180molecular_functioncarboxypeptidase activity
C0004185molecular_functionserine-type carboxypeptidase activity
C0005576cellular_componentextracellular region
C0006508biological_processproteolysis
C0008233molecular_functionpeptidase activity
C0008360biological_processregulation of cell shape
C0009002molecular_functionserine-type D-Ala-D-Ala carboxypeptidase activity
C0009252biological_processpeptidoglycan biosynthetic process
C0016787molecular_functionhydrolase activity
C0046677biological_processresponse to antibiotic
C0071555biological_processcell wall organization
D0000270biological_processpeptidoglycan metabolic process
D0004180molecular_functioncarboxypeptidase activity
D0004185molecular_functionserine-type carboxypeptidase activity
D0005576cellular_componentextracellular region
D0006508biological_processproteolysis
D0008233molecular_functionpeptidase activity
D0008360biological_processregulation of cell shape
D0009002molecular_functionserine-type D-Ala-D-Ala carboxypeptidase activity
D0009252biological_processpeptidoglycan biosynthetic process
D0016787molecular_functionhydrolase activity
D0046677biological_processresponse to antibiotic
D0071555biological_processcell wall organization
Functional Information from PDB Data
site_idAC1
Number of Residues4
DetailsBINDING SITE FOR RESIDUE SO4 A 1467
ChainResidue
AHIS282
ATHR283
AHOH2209
AHOH2210

site_idAC2
Number of Residues3
DetailsBINDING SITE FOR RESIDUE SO4 A 1468
ChainResidue
AALA234
AARG236
AHOH2278

site_idAC3
Number of Residues3
DetailsBINDING SITE FOR RESIDUE SO4 A 1469
ChainResidue
ALEU134
ASER131
AARG133

site_idAC4
Number of Residues6
DetailsBINDING SITE FOR RESIDUE SO4 A 1470
ChainResidue
AGLY159
AGLU160
AARG161
ASO41473
AHOH2133
AHOH2280

site_idAC5
Number of Residues3
DetailsBINDING SITE FOR RESIDUE MG A 610
ChainResidue
AGLU188
AHIS247
AGLU251

site_idAC6
Number of Residues1
DetailsBINDING SITE FOR RESIDUE MG A 611
ChainResidue
AGLU404

site_idAC7
Number of Residues2
DetailsBINDING SITE FOR RESIDUE SO4 B 1466
ChainResidue
BHIS282
BTHR283

site_idAC8
Number of Residues5
DetailsBINDING SITE FOR RESIDUE SO4 B 1467
ChainResidue
BALA234
BARG236
BHOH2180
BHOH2271
BHOH2272

site_idAC9
Number of Residues3
DetailsBINDING SITE FOR RESIDUE SO4 B 1468
ChainResidue
BSER131
BARG133
BLEU134

site_idBC1
Number of Residues5
DetailsBINDING SITE FOR RESIDUE SO4 B 1469
ChainResidue
BGLY159
BGLU160
BARG161
BSO41472
BHOH2131

site_idBC2
Number of Residues3
DetailsBINDING SITE FOR RESIDUE SO4 C 1466
ChainResidue
CHIS282
CTHR283
CHOH2087

site_idBC3
Number of Residues2
DetailsBINDING SITE FOR RESIDUE SO4 C 1467
ChainResidue
CARG236
CHOH2294

site_idBC4
Number of Residues5
DetailsBINDING SITE FOR RESIDUE SO4 C 1468
ChainResidue
CSER131
CGLU132
CARG133
CLEU134
CHOH2103

site_idBC5
Number of Residues5
DetailsBINDING SITE FOR RESIDUE SO4 C 1469
ChainResidue
CGLY159
CGLU160
CARG161
CSO41472
CHOH2145

site_idBC6
Number of Residues4
DetailsBINDING SITE FOR RESIDUE SO4 D 1467
ChainResidue
DASP281
DHIS282
DTHR283
DHOH2053

site_idBC7
Number of Residues3
DetailsBINDING SITE FOR RESIDUE SO4 D 1468
ChainResidue
DALA234
DARG236
DHOH2199

site_idBC8
Number of Residues6
DetailsBINDING SITE FOR RESIDUE SO4 D 1469
ChainResidue
DSER131
DARG133
DLEU134
DHOH2201
DHOH2202
DHOH2203

site_idBC9
Number of Residues5
DetailsBINDING SITE FOR RESIDUE SO4 D 1470
ChainResidue
DGLY159
DGLU160
DARG161
DSO41471
DHOH2106

site_idCC1
Number of Residues3
DetailsBINDING SITE FOR RESIDUE MG D 610
ChainResidue
DGLU188
DHIS247
DGLU251

site_idCC2
Number of Residues2
DetailsBINDING SITE FOR RESIDUE MG D 611
ChainResidue
DVAL406
DHIS462

site_idCC3
Number of Residues4
DetailsBINDING SITE FOR RESIDUE SO4 C 1470
ChainResidue
CHIS158
CGLY159
CSO41472
CHOH2082

site_idCC4
Number of Residues3
DetailsBINDING SITE FOR RESIDUE SO4 A 1471
ChainResidue
AARG39
AASP40
AHOH2023

site_idCC5
Number of Residues3
DetailsBINDING SITE FOR RESIDUE SO4 A 1472
ChainResidue
AGLU192
ALEU193
AHOH2156

site_idCC6
Number of Residues2
DetailsBINDING SITE FOR RESIDUE SO4 B 1470
ChainResidue
BARG39
BASP40

site_idCC7
Number of Residues3
DetailsBINDING SITE FOR RESIDUE SO4 B 1471
ChainResidue
BTRP139
BSER415
BHOH2257

site_idCC8
Number of Residues3
DetailsBINDING SITE FOR RESIDUE SO4 C 1471
ChainResidue
CTHR413
CHOH2122
CHOH2134

site_idCC9
Number of Residues5
DetailsBINDING SITE FOR RESIDUE SO4 B 1472
ChainResidue
AGLY203
BHIS158
BGLU168
BLEU235
BSO41469

site_idDC1
Number of Residues4
DetailsBINDING SITE FOR RESIDUE SO4 C 1472
ChainResidue
CSO41470
CHIS158
CGLU168
CSO41469

site_idDC2
Number of Residues4
DetailsBINDING SITE FOR RESIDUE SO4 D 1471
ChainResidue
DHIS158
DGLU168
DSO41470
DHOH2104

site_idDC3
Number of Residues6
DetailsBINDING SITE FOR RESIDUE SO4 A 1473
ChainResidue
AHIS158
AGLU168
ASO41470
AHOH2146
AHOH2279
AHOH2280

site_idDC4
Number of Residues10
DetailsBinding site for Ligand BSF A 500 bound to SER A 49
ChainResidue
ASER49
ALYS52
APHE297
ASER298
ALYS410
ATHR411
AGLY412
ATHR413
AHOH2028
BALA175

site_idDC5
Number of Residues10
DetailsBinding site for Ligand BSF A 500 bound to SER A 298
ChainResidue
ASER49
ALYS52
APHE297
ASER298
ALYS410
ATHR411
AGLY412
ATHR413
AHOH2028
BALA175

site_idDC6
Number of Residues9
DetailsBinding site for Ligand BSF B 500 bound to SER B 49
ChainResidue
BSER49
BLYS52
BSER298
BLYS410
BTHR411
BGLY412
BTHR413
BHOH2204
BHOH2206

site_idDC7
Number of Residues9
DetailsBinding site for Ligand BSF B 500 bound to SER B 298
ChainResidue
BSER49
BLYS52
BSER298
BLYS410
BTHR411
BGLY412
BTHR413
BHOH2204
BHOH2206

site_idDC8
Number of Residues9
DetailsBinding site for Ligand BSF C 500 bound to SER C 49
ChainResidue
CSER49
CPHE297
CSER298
CLYS410
CTHR411
CGLY412
CTHR413
CHOH2229
CHOH2276

site_idDC9
Number of Residues9
DetailsBinding site for Ligand BSF C 500 bound to SER C 298
ChainResidue
CSER49
CPHE297
CSER298
CLYS410
CTHR411
CGLY412
CTHR413
CHOH2229
CHOH2276

site_idEC1
Number of Residues9
DetailsBinding site for Ligand BSF D 500 bound to SER D 49
ChainResidue
DSER49
DLYS52
DSER298
DLYS410
DTHR411
DGLY412
DTHR413
DHOH2016
DHOH2187

site_idEC2
Number of Residues9
DetailsBinding site for Ligand BSF D 500 bound to SER D 298
ChainResidue
DSER49
DLYS52
DSER298
DLYS410
DTHR411
DGLY412
DTHR413
DHOH2016
DHOH2187

Functional Information from SwissProt/UniProt
site_idSWS_FT_FI1
Number of Residues692
DetailsRegion: {"description":"Absent in class-A beta-lactamases"}
ChainResidueDetails

site_idSWS_FT_FI2
Number of Residues4
DetailsActive site: {"description":"Acyl-ester intermediate"}
ChainResidueDetails

site_idSWS_FT_FI3
Number of Residues4
DetailsActive site: {"description":"Proton acceptor"}
ChainResidueDetails

site_idSWS_FT_FI4
Number of Residues4
DetailsActive site: {"evidences":[{"evidenceCode":"ECO:0000250"}]}
ChainResidueDetails

site_idSWS_FT_FI5
Number of Residues4
DetailsBinding site: {}
ChainResidueDetails

239149

PDB entries from 2025-07-23

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