2XDM
Crystal structure of a complex between Actinomadura R39 DD peptidase and a peptidoglycan mimetic 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 | 7 |
| Details | BINDING SITE FOR RESIDUE SO4 A 600 |
| Chain | Residue |
| A | SER49 |
| A | SER298 |
| A | THR393 |
| A | LYS410 |
| A | THR411 |
| A | GLY412 |
| A | THR413 |
| site_id | AC2 |
| Number of Residues | 4 |
| Details | BINDING SITE FOR RESIDUE SO4 A 601 |
| Chain | Residue |
| A | THR283 |
| A | HOH2178 |
| A | ASP281 |
| A | HIS282 |
| site_id | AC3 |
| Number of Residues | 2 |
| Details | BINDING SITE FOR RESIDUE SO4 A 602 |
| Chain | Residue |
| A | ARG236 |
| A | HOH2179 |
| site_id | AC4 |
| Number of Residues | 3 |
| Details | BINDING SITE FOR RESIDUE SO4 A 603 |
| Chain | Residue |
| A | SER131 |
| A | ARG133 |
| A | LEU134 |
| site_id | AC5 |
| Number of Residues | 5 |
| Details | BINDING SITE FOR RESIDUE SO4 A 604 |
| Chain | Residue |
| A | GLY159 |
| A | GLU160 |
| A | ARG161 |
| A | HOH2073 |
| A | HOH2181 |
| site_id | AC6 |
| Number of Residues | 3 |
| Details | BINDING SITE FOR RESIDUE CO A 610 |
| Chain | Residue |
| A | GLU188 |
| A | HIS247 |
| A | GLU251 |
| site_id | AC7 |
| Number of Residues | 4 |
| Details | BINDING SITE FOR RESIDUE CO A 611 |
| Chain | Residue |
| A | ALA402 |
| A | VAL406 |
| A | HIS462 |
| A | GLN463 |
| site_id | AC8 |
| Number of Residues | 17 |
| Details | BINDING SITE FOR RESIDUE BO8 B 500 |
| Chain | Residue |
| B | ALA48 |
| B | SER49 |
| B | TRP139 |
| B | ASP142 |
| B | TYR147 |
| B | SER298 |
| B | ASN300 |
| B | GLY348 |
| B | LEU349 |
| B | ARG351 |
| B | GLY412 |
| B | THR413 |
| B | MET414 |
| B | SER415 |
| B | SO4600 |
| B | HOH2110 |
| B | HOH2111 |
| site_id | AC9 |
| Number of Residues | 7 |
| Details | BINDING SITE FOR RESIDUE SO4 B 600 |
| Chain | Residue |
| B | SER298 |
| B | THR393 |
| B | LYS410 |
| B | THR411 |
| B | GLY412 |
| B | THR413 |
| B | BO8500 |
| site_id | BC1 |
| Number of Residues | 3 |
| Details | BINDING SITE FOR RESIDUE SO4 B 601 |
| Chain | Residue |
| B | HIS282 |
| B | THR283 |
| B | HOH2113 |
| site_id | BC2 |
| Number of Residues | 3 |
| Details | BINDING SITE FOR RESIDUE SO4 B 602 |
| Chain | Residue |
| B | ARG236 |
| B | HOH2115 |
| B | HOH2117 |
| site_id | BC3 |
| Number of Residues | 3 |
| Details | BINDING SITE FOR RESIDUE SO4 B 603 |
| Chain | Residue |
| B | GLU132 |
| B | ARG133 |
| B | LEU134 |
| site_id | BC4 |
| Number of Residues | 5 |
| Details | BINDING SITE FOR RESIDUE SO4 B 604 |
| Chain | Residue |
| B | GLY159 |
| B | GLU160 |
| B | ARG161 |
| B | HOH2049 |
| B | HOH2119 |
| site_id | BC5 |
| Number of Residues | 16 |
| Details | BINDING SITE FOR RESIDUE BO8 C 500 |
| Chain | Residue |
| C | SER49 |
| C | LYS52 |
| C | TRP139 |
| C | ASP142 |
| C | TYR147 |
| C | SER298 |
| C | ASN300 |
| C | SER347 |
| C | GLY348 |
| C | LEU349 |
| C | ARG351 |
| C | GLY412 |
| C | THR413 |
| C | SER415 |
| C | SO4600 |
| C | HOH2142 |
| site_id | BC6 |
| Number of Residues | 6 |
| Details | BINDING SITE FOR RESIDUE SO4 C 600 |
| Chain | Residue |
| C | SER298 |
| C | LYS410 |
| C | THR411 |
| C | GLY412 |
| C | THR413 |
| C | BO8500 |
| site_id | BC7 |
| Number of Residues | 3 |
| Details | BINDING SITE FOR RESIDUE SO4 C 601 |
| Chain | Residue |
| C | ASP281 |
| C | HIS282 |
| C | THR283 |
| site_id | BC8 |
| Number of Residues | 1 |
| Details | BINDING SITE FOR RESIDUE SO4 C 602 |
| Chain | Residue |
| C | ARG236 |
| site_id | BC9 |
| Number of Residues | 3 |
| Details | BINDING SITE FOR RESIDUE SO4 C 603 |
| Chain | Residue |
| C | SER131 |
| C | ARG133 |
| C | LEU134 |
| site_id | CC1 |
| Number of Residues | 3 |
| Details | BINDING SITE FOR RESIDUE SO4 C 604 |
| Chain | Residue |
| C | GLY159 |
| C | GLU160 |
| C | ARG161 |
| site_id | CC2 |
| Number of Residues | 7 |
| Details | BINDING SITE FOR RESIDUE SO4 D 600 |
| Chain | Residue |
| D | SER298 |
| D | THR393 |
| D | LYS410 |
| D | THR411 |
| D | GLY412 |
| D | THR413 |
| D | SER49 |
| site_id | CC3 |
| Number of Residues | 3 |
| Details | BINDING SITE FOR RESIDUE SO4 D 601 |
| Chain | Residue |
| D | ASP281 |
| D | HIS282 |
| D | THR283 |
| site_id | CC4 |
| Number of Residues | 3 |
| Details | BINDING SITE FOR RESIDUE SO4 D 602 |
| Chain | Residue |
| D | ALA234 |
| D | ARG236 |
| D | HOH2110 |
| site_id | CC5 |
| Number of Residues | 7 |
| Details | BINDING SITE FOR RESIDUE SO4 D 603 |
| Chain | Residue |
| D | SER131 |
| D | GLU132 |
| D | ARG133 |
| D | LEU134 |
| D | HOH2111 |
| D | HOH2112 |
| D | HOH2113 |
| site_id | CC6 |
| Number of Residues | 3 |
| Details | BINDING SITE FOR RESIDUE SO4 D 604 |
| Chain | Residue |
| D | GLY159 |
| D | GLU160 |
| D | ARG161 |
| site_id | CC7 |
| Number of Residues | 3 |
| Details | BINDING SITE FOR RESIDUE CO D 610 |
| Chain | Residue |
| D | GLU188 |
| D | HIS247 |
| D | GLU251 |
| site_id | CC8 |
| Number of Residues | 2 |
| Details | BINDING SITE FOR RESIDUE CO D 611 |
| Chain | Residue |
| D | VAL406 |
| D | HIS462 |
| site_id | CC9 |
| Number of Residues | 5 |
| Details | BINDING SITE FOR RESIDUE MES D 1467 |
| Chain | Residue |
| D | ALA373 |
| D | TRP376 |
| D | SER377 |
| D | TYR423 |
| D | GLU430 |
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 |
