4B4Z
Crystal structure of a complex between Actinomadura R39 DD-peptidase and a sulfonamide boronate inhibitor
Functional Information from GO Data
| Chain | GOid | namespace | contents |
| A | 0004180 | molecular_function | carboxypeptidase activity |
| A | 0004185 | molecular_function | serine-type carboxypeptidase activity |
| A | 0005576 | cellular_component | extracellular region |
| A | 0006508 | biological_process | proteolysis |
| A | 0008360 | biological_process | regulation of cell shape |
| A | 0009002 | molecular_function | serine-type D-Ala-D-Ala carboxypeptidase activity |
| A | 0009252 | biological_process | peptidoglycan biosynthetic process |
| A | 0046677 | biological_process | response to antibiotic |
| A | 0071555 | biological_process | cell wall organization |
| B | 0004180 | molecular_function | carboxypeptidase activity |
| B | 0004185 | molecular_function | serine-type carboxypeptidase activity |
| B | 0005576 | cellular_component | extracellular region |
| B | 0006508 | biological_process | proteolysis |
| B | 0008360 | biological_process | regulation of cell shape |
| B | 0009002 | molecular_function | serine-type D-Ala-D-Ala carboxypeptidase activity |
| B | 0009252 | biological_process | peptidoglycan biosynthetic process |
| B | 0046677 | biological_process | response to antibiotic |
| B | 0071555 | biological_process | cell wall organization |
| C | 0004180 | molecular_function | carboxypeptidase activity |
| C | 0004185 | molecular_function | serine-type carboxypeptidase activity |
| C | 0005576 | cellular_component | extracellular region |
| C | 0006508 | biological_process | proteolysis |
| C | 0008360 | biological_process | regulation of cell shape |
| C | 0009002 | molecular_function | serine-type D-Ala-D-Ala carboxypeptidase activity |
| C | 0009252 | biological_process | peptidoglycan biosynthetic process |
| C | 0046677 | biological_process | response to antibiotic |
| C | 0071555 | biological_process | cell wall organization |
| D | 0004180 | molecular_function | carboxypeptidase activity |
| D | 0004185 | molecular_function | serine-type carboxypeptidase activity |
| D | 0005576 | cellular_component | extracellular region |
| D | 0006508 | biological_process | proteolysis |
| D | 0008360 | biological_process | regulation of cell shape |
| D | 0009002 | molecular_function | serine-type D-Ala-D-Ala carboxypeptidase activity |
| D | 0009252 | biological_process | peptidoglycan biosynthetic process |
| D | 0046677 | biological_process | response to antibiotic |
| D | 0071555 | biological_process | cell wall organization |
Functional Information from PDB Data
| site_id | AC1 |
| Number of Residues | 4 |
| Details | BINDING SITE FOR RESIDUE SO4 A 1467 |
| Chain | Residue |
| A | HIS282 |
| A | THR283 |
| A | HOH2209 |
| A | HOH2210 |
| site_id | AC2 |
| Number of Residues | 3 |
| Details | BINDING SITE FOR RESIDUE SO4 A 1468 |
| Chain | Residue |
| A | ALA234 |
| A | ARG236 |
| A | HOH2278 |
| site_id | AC3 |
| Number of Residues | 3 |
| Details | BINDING SITE FOR RESIDUE SO4 A 1469 |
| Chain | Residue |
| A | LEU134 |
| A | SER131 |
| A | ARG133 |
| site_id | AC4 |
| Number of Residues | 6 |
| Details | BINDING SITE FOR RESIDUE SO4 A 1470 |
| Chain | Residue |
| A | GLY159 |
| A | GLU160 |
| A | ARG161 |
| A | SO41473 |
| A | HOH2133 |
| A | HOH2280 |
| site_id | AC5 |
| Number of Residues | 3 |
| Details | BINDING SITE FOR RESIDUE MG A 610 |
| Chain | Residue |
| A | GLU188 |
| A | HIS247 |
| A | GLU251 |
| site_id | AC6 |
| Number of Residues | 1 |
| Details | BINDING SITE FOR RESIDUE MG A 611 |
| Chain | Residue |
| A | GLU404 |
| site_id | AC7 |
| Number of Residues | 2 |
| Details | BINDING SITE FOR RESIDUE SO4 B 1466 |
| Chain | Residue |
| B | HIS282 |
| B | THR283 |
| site_id | AC8 |
| Number of Residues | 5 |
| Details | BINDING SITE FOR RESIDUE SO4 B 1467 |
| Chain | Residue |
| B | ALA234 |
| B | ARG236 |
| B | HOH2180 |
| B | HOH2271 |
| B | HOH2272 |
| site_id | AC9 |
| Number of Residues | 3 |
| Details | BINDING SITE FOR RESIDUE SO4 B 1468 |
| Chain | Residue |
| B | SER131 |
| B | ARG133 |
| B | LEU134 |
| site_id | BC1 |
| Number of Residues | 5 |
| Details | BINDING SITE FOR RESIDUE SO4 B 1469 |
| Chain | Residue |
| B | GLY159 |
| B | GLU160 |
| B | ARG161 |
| B | SO41472 |
| B | HOH2131 |
| site_id | BC2 |
| Number of Residues | 3 |
| Details | BINDING SITE FOR RESIDUE SO4 C 1466 |
| Chain | Residue |
| C | HIS282 |
| C | THR283 |
| C | HOH2087 |
| site_id | BC3 |
| Number of Residues | 2 |
| Details | BINDING SITE FOR RESIDUE SO4 C 1467 |
| Chain | Residue |
| C | ARG236 |
| C | HOH2294 |
| site_id | BC4 |
| Number of Residues | 5 |
| Details | BINDING SITE FOR RESIDUE SO4 C 1468 |
| Chain | Residue |
| C | SER131 |
| C | GLU132 |
| C | ARG133 |
| C | LEU134 |
| C | HOH2103 |
| site_id | BC5 |
| Number of Residues | 5 |
| Details | BINDING SITE FOR RESIDUE SO4 C 1469 |
| Chain | Residue |
| C | GLY159 |
| C | GLU160 |
| C | ARG161 |
| C | SO41472 |
| C | HOH2145 |
| site_id | BC6 |
| Number of Residues | 4 |
| Details | BINDING SITE FOR RESIDUE SO4 D 1467 |
| Chain | Residue |
| D | ASP281 |
| D | HIS282 |
| D | THR283 |
| D | HOH2053 |
| site_id | BC7 |
| Number of Residues | 3 |
| Details | BINDING SITE FOR RESIDUE SO4 D 1468 |
| Chain | Residue |
| D | ALA234 |
| D | ARG236 |
| D | HOH2199 |
| site_id | BC8 |
| Number of Residues | 6 |
| Details | BINDING SITE FOR RESIDUE SO4 D 1469 |
| Chain | Residue |
| D | SER131 |
| D | ARG133 |
| D | LEU134 |
| D | HOH2201 |
| D | HOH2202 |
| D | HOH2203 |
| site_id | BC9 |
| Number of Residues | 5 |
| Details | BINDING SITE FOR RESIDUE SO4 D 1470 |
| Chain | Residue |
| D | GLY159 |
| D | GLU160 |
| D | ARG161 |
| D | SO41471 |
| D | HOH2106 |
| site_id | CC1 |
| Number of Residues | 3 |
| Details | BINDING SITE FOR RESIDUE MG D 610 |
| Chain | Residue |
| D | GLU188 |
| D | HIS247 |
| D | GLU251 |
| site_id | CC2 |
| Number of Residues | 2 |
| Details | BINDING SITE FOR RESIDUE MG D 611 |
| Chain | Residue |
| D | VAL406 |
| D | HIS462 |
| site_id | CC3 |
| Number of Residues | 4 |
| Details | BINDING SITE FOR RESIDUE SO4 C 1470 |
| Chain | Residue |
| C | HIS158 |
| C | GLY159 |
| C | SO41472 |
| C | HOH2082 |
| site_id | CC4 |
| Number of Residues | 3 |
| Details | BINDING SITE FOR RESIDUE SO4 A 1471 |
| Chain | Residue |
| A | ARG39 |
| A | ASP40 |
| A | HOH2023 |
| site_id | CC5 |
| Number of Residues | 3 |
| Details | BINDING SITE FOR RESIDUE SO4 A 1472 |
| Chain | Residue |
| A | GLU192 |
| A | LEU193 |
| A | HOH2156 |
| site_id | CC6 |
| Number of Residues | 2 |
| Details | BINDING SITE FOR RESIDUE SO4 B 1470 |
| Chain | Residue |
| B | ARG39 |
| B | ASP40 |
| site_id | CC7 |
| Number of Residues | 3 |
| Details | BINDING SITE FOR RESIDUE SO4 B 1471 |
| Chain | Residue |
| B | TRP139 |
| B | SER415 |
| B | HOH2257 |
| site_id | CC8 |
| Number of Residues | 3 |
| Details | BINDING SITE FOR RESIDUE SO4 C 1471 |
| Chain | Residue |
| C | THR413 |
| C | HOH2122 |
| C | HOH2134 |
| site_id | CC9 |
| Number of Residues | 5 |
| Details | BINDING SITE FOR RESIDUE SO4 B 1472 |
| Chain | Residue |
| A | GLY203 |
| B | HIS158 |
| B | GLU168 |
| B | LEU235 |
| B | SO41469 |
| site_id | DC1 |
| Number of Residues | 4 |
| Details | BINDING SITE FOR RESIDUE SO4 C 1472 |
| Chain | Residue |
| C | SO41470 |
| C | HIS158 |
| C | GLU168 |
| C | SO41469 |
| site_id | DC2 |
| Number of Residues | 4 |
| Details | BINDING SITE FOR RESIDUE SO4 D 1471 |
| Chain | Residue |
| D | HIS158 |
| D | GLU168 |
| D | SO41470 |
| D | HOH2104 |
| site_id | DC3 |
| Number of Residues | 6 |
| Details | BINDING SITE FOR RESIDUE SO4 A 1473 |
| Chain | Residue |
| A | HIS158 |
| A | GLU168 |
| A | SO41470 |
| A | HOH2146 |
| A | HOH2279 |
| A | HOH2280 |
| site_id | DC4 |
| Number of Residues | 10 |
| Details | Binding site for Ligand BSF A 500 bound to SER A 49 |
| Chain | Residue |
| A | SER49 |
| A | LYS52 |
| A | PHE297 |
| A | SER298 |
| A | LYS410 |
| A | THR411 |
| A | GLY412 |
| A | THR413 |
| A | HOH2028 |
| B | ALA175 |
| site_id | DC5 |
| Number of Residues | 10 |
| Details | Binding site for Ligand BSF A 500 bound to SER A 298 |
| Chain | Residue |
| A | SER49 |
| A | LYS52 |
| A | PHE297 |
| A | SER298 |
| A | LYS410 |
| A | THR411 |
| A | GLY412 |
| A | THR413 |
| A | HOH2028 |
| B | ALA175 |
| site_id | DC6 |
| Number of Residues | 9 |
| Details | Binding site for Ligand BSF B 500 bound to SER B 49 |
| Chain | Residue |
| B | SER49 |
| B | LYS52 |
| B | SER298 |
| B | LYS410 |
| B | THR411 |
| B | GLY412 |
| B | THR413 |
| B | HOH2204 |
| B | HOH2206 |
| site_id | DC7 |
| Number of Residues | 9 |
| Details | Binding site for Ligand BSF B 500 bound to SER B 298 |
| Chain | Residue |
| B | SER49 |
| B | LYS52 |
| B | SER298 |
| B | LYS410 |
| B | THR411 |
| B | GLY412 |
| B | THR413 |
| B | HOH2204 |
| B | HOH2206 |
| site_id | DC8 |
| Number of Residues | 9 |
| Details | Binding site for Ligand BSF C 500 bound to SER C 49 |
| Chain | Residue |
| C | SER49 |
| C | PHE297 |
| C | SER298 |
| C | LYS410 |
| C | THR411 |
| C | GLY412 |
| C | THR413 |
| C | HOH2229 |
| C | HOH2276 |
| site_id | DC9 |
| Number of Residues | 9 |
| Details | Binding site for Ligand BSF C 500 bound to SER C 298 |
| Chain | Residue |
| C | SER49 |
| C | PHE297 |
| C | SER298 |
| C | LYS410 |
| C | THR411 |
| C | GLY412 |
| C | THR413 |
| C | HOH2229 |
| C | HOH2276 |
| site_id | EC1 |
| Number of Residues | 9 |
| Details | Binding site for Ligand BSF D 500 bound to SER D 49 |
| Chain | Residue |
| D | SER49 |
| D | LYS52 |
| D | SER298 |
| D | LYS410 |
| D | THR411 |
| D | GLY412 |
| D | THR413 |
| D | HOH2016 |
| D | HOH2187 |
| site_id | EC2 |
| Number of Residues | 9 |
| Details | Binding site for Ligand BSF D 500 bound to SER D 298 |
| Chain | Residue |
| D | SER49 |
| D | LYS52 |
| D | SER298 |
| D | LYS410 |
| D | THR411 |
| D | GLY412 |
| D | THR413 |
| D | HOH2016 |
| D | HOH2187 |
Functional Information from SwissProt/UniProt
| site_id | SWS_FT_FI1 |
| Number of Residues | 4 |
| Details | ACT_SITE: Acyl-ester intermediate |
| Chain | Residue | Details |
| A | SER49 | |
| B | SER49 | |
| C | SER49 | |
| D | SER49 |
| site_id | SWS_FT_FI2 |
| Number of Residues | 4 |
| Details | ACT_SITE: Proton acceptor |
| Chain | Residue | Details |
| A | LYS52 | |
| B | LYS52 | |
| C | LYS52 | |
| D | LYS52 |
| site_id | SWS_FT_FI3 |
| Number of Residues | 4 |
| Details | ACT_SITE: ACT_SITE => ECO:0000250 |
| Chain | Residue | Details |
| A | SER298 | |
| B | SER298 | |
| C | SER298 | |
| D | SER298 |
| site_id | SWS_FT_FI4 |
| Number of Residues | 4 |
| Details | BINDING: |
| Chain | Residue | Details |
| A | LYS410 | |
| B | LYS410 | |
| C | LYS410 | |
| D | LYS410 |
