4B4X
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 | 0000270 | biological_process | peptidoglycan metabolic process |
| 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 | 0008233 | molecular_function | peptidase activity |
| 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 | 0016787 | molecular_function | hydrolase activity |
| A | 0046677 | biological_process | response to antibiotic |
| A | 0071555 | biological_process | cell wall organization |
| B | 0000270 | biological_process | peptidoglycan metabolic process |
| 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 | 0008233 | molecular_function | peptidase activity |
| 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 | 0016787 | molecular_function | hydrolase activity |
| B | 0046677 | biological_process | response to antibiotic |
| B | 0071555 | biological_process | cell wall organization |
| C | 0000270 | biological_process | peptidoglycan metabolic process |
| 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 | 0008233 | molecular_function | peptidase activity |
| 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 | 0016787 | molecular_function | hydrolase activity |
| C | 0046677 | biological_process | response to antibiotic |
| C | 0071555 | biological_process | cell wall organization |
| D | 0000270 | biological_process | peptidoglycan metabolic process |
| 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 | 0008233 | molecular_function | peptidase activity |
| 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 | 0016787 | molecular_function | hydrolase activity |
| 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 | 8 |
| Details | BINDING SITE FOR RESIDUE HQZ A 500 |
| Chain | Residue |
| A | SER49 |
| A | TYR147 |
| A | SER298 |
| A | ASN300 |
| A | THR413 |
| A | MET414 |
| A | HOH2068 |
| B | GLU176 |
| site_id | AC2 |
| Number of Residues | 3 |
| Details | BINDING SITE FOR RESIDUE SO4 A 1467 |
| Chain | Residue |
| A | THR283 |
| A | HOH2087 |
| A | HIS282 |
| site_id | AC3 |
| Number of Residues | 5 |
| Details | BINDING SITE FOR RESIDUE SO4 A 1468 |
| Chain | Residue |
| A | ALA234 |
| A | LEU235 |
| A | ARG236 |
| A | HOH2054 |
| A | HOH2088 |
| site_id | AC4 |
| Number of Residues | 4 |
| Details | BINDING SITE FOR RESIDUE SO4 A 1469 |
| Chain | Residue |
| A | SER131 |
| A | GLU132 |
| A | ARG133 |
| A | LEU134 |
| site_id | AC5 |
| Number of Residues | 4 |
| Details | BINDING SITE FOR RESIDUE SO4 A 1470 |
| Chain | Residue |
| A | HIS158 |
| A | GLU168 |
| A | HOH2037 |
| A | HOH2090 |
| site_id | AC6 |
| Number of Residues | 4 |
| Details | BINDING SITE FOR RESIDUE MG A 1471 |
| Chain | Residue |
| A | ALA186 |
| A | GLU188 |
| A | HIS247 |
| A | GLU251 |
| site_id | AC7 |
| Number of Residues | 2 |
| Details | BINDING SITE FOR RESIDUE MG A 1472 |
| Chain | Residue |
| A | VAL406 |
| A | HIS462 |
| site_id | AC8 |
| Number of Residues | 3 |
| Details | BINDING SITE FOR RESIDUE SO4 A 1473 |
| Chain | Residue |
| A | GLU101 |
| A | HIS158 |
| A | GLY159 |
| site_id | AC9 |
| Number of Residues | 3 |
| Details | BINDING SITE FOR RESIDUE SO4 A 1474 |
| Chain | Residue |
| A | THR97 |
| A | ASP102 |
| A | HIS282 |
| site_id | BC1 |
| Number of Residues | 7 |
| Details | BINDING SITE FOR RESIDUE HQZ B 500 |
| Chain | Residue |
| B | SER49 |
| B | TYR147 |
| B | SER298 |
| B | ASN300 |
| B | GLY412 |
| B | THR413 |
| B | HOH2053 |
| site_id | BC2 |
| Number of Residues | 2 |
| Details | BINDING SITE FOR RESIDUE SO4 B 1466 |
| Chain | Residue |
| B | HIS282 |
| B | THR283 |
| site_id | BC3 |
| Number of Residues | 3 |
| Details | BINDING SITE FOR RESIDUE SO4 B 1467 |
| Chain | Residue |
| B | ALA234 |
| B | ARG236 |
| B | HOH2047 |
| site_id | BC4 |
| Number of Residues | 4 |
| Details | BINDING SITE FOR RESIDUE SO4 B 1468 |
| Chain | Residue |
| B | SER131 |
| B | GLU132 |
| B | ARG133 |
| B | LEU134 |
| site_id | BC5 |
| Number of Residues | 3 |
| Details | BINDING SITE FOR RESIDUE SO4 B 1469 |
| Chain | Residue |
| B | HIS158 |
| B | GLY159 |
| B | SO41470 |
| site_id | BC6 |
| Number of Residues | 6 |
| Details | BINDING SITE FOR RESIDUE SO4 B 1470 |
| Chain | Residue |
| A | GLY203 |
| B | HIS158 |
| B | GLU168 |
| B | SO41469 |
| B | HOH2033 |
| B | HOH2066 |
| site_id | BC7 |
| Number of Residues | 5 |
| Details | BINDING SITE FOR RESIDUE SO4 B 1471 |
| Chain | Residue |
| B | ASP95 |
| B | THR97 |
| B | ASP102 |
| B | HIS282 |
| B | SER284 |
| site_id | BC8 |
| Number of Residues | 8 |
| Details | BINDING SITE FOR RESIDUE HQZ C 500 |
| Chain | Residue |
| C | ALA48 |
| C | SER49 |
| C | TYR147 |
| C | SER298 |
| C | ASN300 |
| C | LEU349 |
| C | GLY412 |
| C | THR413 |
| site_id | BC9 |
| Number of Residues | 4 |
| Details | BINDING SITE FOR RESIDUE SO4 C 1466 |
| Chain | Residue |
| C | ASP95 |
| C | THR97 |
| C | ASP102 |
| C | HIS282 |
| site_id | CC1 |
| Number of Residues | 2 |
| Details | BINDING SITE FOR RESIDUE SO4 C 1467 |
| Chain | Residue |
| C | ARG236 |
| C | HOH2072 |
| site_id | CC2 |
| Number of Residues | 3 |
| Details | BINDING SITE FOR RESIDUE SO4 C 1468 |
| Chain | Residue |
| C | SER131 |
| C | ARG133 |
| C | LEU134 |
| site_id | CC3 |
| Number of Residues | 4 |
| Details | BINDING SITE FOR RESIDUE SO4 C 1469 |
| Chain | Residue |
| C | GLY159 |
| C | GLU160 |
| C | ARG161 |
| C | HOH2034 |
| site_id | CC4 |
| Number of Residues | 3 |
| Details | BINDING SITE FOR RESIDUE SO4 C 1470 |
| Chain | Residue |
| C | ASP281 |
| C | HIS282 |
| C | THR283 |
| site_id | CC5 |
| Number of Residues | 2 |
| Details | BINDING SITE FOR RESIDUE SO4 C 1471 |
| Chain | Residue |
| C | HIS158 |
| C | GLY159 |
| site_id | CC6 |
| Number of Residues | 6 |
| Details | BINDING SITE FOR RESIDUE HQZ D 500 |
| Chain | Residue |
| D | SER49 |
| D | TYR147 |
| D | SER298 |
| D | ASN300 |
| D | THR413 |
| D | HOH2105 |
| site_id | CC7 |
| Number of Residues | 3 |
| Details | BINDING SITE FOR RESIDUE SO4 D 1467 |
| Chain | Residue |
| D | THR283 |
| D | HOH2077 |
| D | HIS282 |
| site_id | CC8 |
| Number of Residues | 4 |
| Details | BINDING SITE FOR RESIDUE SO4 D 1468 |
| Chain | Residue |
| D | ALA234 |
| D | ARG236 |
| D | HOH2066 |
| D | HOH2106 |
| site_id | CC9 |
| Number of Residues | 5 |
| Details | BINDING SITE FOR RESIDUE SO4 D 1469 |
| Chain | Residue |
| D | SER131 |
| D | GLU132 |
| D | ARG133 |
| D | LEU134 |
| D | HOH2107 |
| site_id | DC1 |
| Number of Residues | 3 |
| Details | BINDING SITE FOR RESIDUE SO4 D 1470 |
| Chain | Residue |
| D | HIS158 |
| D | GLU168 |
| D | SO41473 |
| site_id | DC2 |
| Number of Residues | 3 |
| Details | BINDING SITE FOR RESIDUE MG D 1471 |
| Chain | Residue |
| D | GLU188 |
| D | HIS247 |
| D | GLU251 |
| site_id | DC3 |
| Number of Residues | 1 |
| Details | BINDING SITE FOR RESIDUE MG D 1472 |
| Chain | Residue |
| D | HIS462 |
| site_id | DC4 |
| Number of Residues | 3 |
| Details | BINDING SITE FOR RESIDUE SO4 D 1473 |
| Chain | Residue |
| D | HIS158 |
| D | GLY159 |
| D | SO41470 |
| site_id | DC5 |
| Number of Residues | 6 |
| Details | BINDING SITE FOR RESIDUE SO4 D 1474 |
| Chain | Residue |
| D | ASP95 |
| D | THR97 |
| D | ASP102 |
| D | HIS282 |
| D | SER284 |
| D | ALA285 |
Functional Information from SwissProt/UniProt
| site_id | SWS_FT_FI1 |
| Number of Residues | 692 |
| Details | Region: {"description":"Absent in class-A beta-lactamases"} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI2 |
| Number of Residues | 4 |
| Details | Active site: {"description":"Acyl-ester intermediate"} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI3 |
| Number of Residues | 4 |
| Details | Active site: {"description":"Proton acceptor"} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI4 |
| Number of Residues | 4 |
| Details | Active site: {"evidences":[{"evidenceCode":"ECO:0000250"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI5 |
| Number of Residues | 4 |
| Details | Binding site: {} |
| Chain | Residue | Details |
