2WKE
Crystal structure of the Actinomadura R39 DD-peptidase inhibited by 6- beta-iodopenicillanate.
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 BIY A 500 |
| Chain | Residue |
| A | ALA48 |
| A | SER49 |
| A | TYR147 |
| A | SER298 |
| A | ASN300 |
| A | GLY412 |
| A | THR413 |
| B | ALA175 |
| site_id | AC2 |
| Number of Residues | 3 |
| Details | BINDING SITE FOR RESIDUE SO4 A 601 |
| Chain | Residue |
| A | THR283 |
| A | HOH2044 |
| A | HIS282 |
| site_id | AC3 |
| Number of Residues | 3 |
| Details | BINDING SITE FOR RESIDUE SO4 A 602 |
| Chain | Residue |
| A | ALA234 |
| A | ARG236 |
| A | HOH2167 |
| site_id | AC4 |
| Number of Residues | 4 |
| Details | BINDING SITE FOR RESIDUE SO4 A 603 |
| Chain | Residue |
| A | ASP211 |
| A | PRO213 |
| A | VAL214 |
| A | HOH2168 |
| site_id | AC5 |
| Number of Residues | 4 |
| Details | BINDING SITE FOR RESIDUE SO4 A 604 |
| Chain | Residue |
| A | SER131 |
| A | GLU132 |
| A | ARG133 |
| A | LEU134 |
| site_id | AC6 |
| Number of Residues | 4 |
| Details | BINDING SITE FOR RESIDUE SO4 A 605 |
| Chain | Residue |
| A | THR97 |
| A | ASP102 |
| A | HIS282 |
| A | HOH2035 |
| site_id | AC7 |
| Number of Residues | 4 |
| Details | BINDING SITE FOR RESIDUE CO A 610 |
| Chain | Residue |
| A | GLU188 |
| A | HIS247 |
| A | GLU251 |
| A | HOH2169 |
| site_id | AC8 |
| Number of Residues | 2 |
| Details | BINDING SITE FOR RESIDUE CO A 611 |
| Chain | Residue |
| A | HIS462 |
| A | HOH2170 |
| site_id | AC9 |
| Number of Residues | 2 |
| Details | BINDING SITE FOR RESIDUE CO A 612 |
| Chain | Residue |
| A | LEU63 |
| A | HIS67 |
| site_id | BC1 |
| Number of Residues | 2 |
| Details | BINDING SITE FOR RESIDUE CO A 613 |
| Chain | Residue |
| A | HIS158 |
| A | GLU168 |
| site_id | BC2 |
| Number of Residues | 9 |
| Details | BINDING SITE FOR RESIDUE BIY B 500 |
| Chain | Residue |
| B | ALA48 |
| B | SER49 |
| B | TYR147 |
| B | SER298 |
| B | ASN300 |
| B | GLY412 |
| B | THR413 |
| B | HOH2129 |
| B | HOH2141 |
| site_id | BC3 |
| Number of Residues | 3 |
| Details | BINDING SITE FOR RESIDUE SO4 B 601 |
| Chain | Residue |
| B | HIS282 |
| B | THR283 |
| B | HOH2098 |
| site_id | BC4 |
| Number of Residues | 2 |
| Details | BINDING SITE FOR RESIDUE SO4 B 602 |
| Chain | Residue |
| B | ALA234 |
| B | ARG236 |
| site_id | BC5 |
| Number of Residues | 3 |
| Details | BINDING SITE FOR RESIDUE SO4 B 603 |
| Chain | Residue |
| B | TRP139 |
| B | SER415 |
| B | HOH2142 |
| site_id | BC6 |
| Number of Residues | 4 |
| Details | BINDING SITE FOR RESIDUE SO4 B 604 |
| Chain | Residue |
| B | SER131 |
| B | ARG133 |
| B | LEU134 |
| B | HOH2143 |
| site_id | BC7 |
| Number of Residues | 5 |
| Details | BINDING SITE FOR RESIDUE SO4 B 605 |
| Chain | Residue |
| B | THR97 |
| B | ASP102 |
| B | HIS282 |
| B | SER284 |
| B | HOH2030 |
| site_id | BC8 |
| Number of Residues | 3 |
| Details | BINDING SITE FOR RESIDUE CO B 610 |
| Chain | Residue |
| B | GLU188 |
| B | HIS247 |
| B | GLU251 |
| site_id | BC9 |
| Number of Residues | 2 |
| Details | BINDING SITE FOR RESIDUE CO B 612 |
| Chain | Residue |
| B | LEU63 |
| B | HIS67 |
| site_id | CC1 |
| Number of Residues | 1 |
| Details | BINDING SITE FOR RESIDUE CO B 613 |
| Chain | Residue |
| B | HIS158 |
| site_id | CC2 |
| Number of Residues | 8 |
| Details | BINDING SITE FOR RESIDUE BIY C 500 |
| Chain | Residue |
| C | ALA48 |
| C | SER49 |
| C | TYR147 |
| C | SER298 |
| C | GLY412 |
| C | THR413 |
| C | HOH2146 |
| C | HOH2147 |
| site_id | CC3 |
| Number of Residues | 2 |
| Details | BINDING SITE FOR RESIDUE SO4 C 601 |
| Chain | Residue |
| C | HIS282 |
| C | THR283 |
| site_id | CC4 |
| Number of Residues | 1 |
| Details | BINDING SITE FOR RESIDUE SO4 C 602 |
| Chain | Residue |
| C | ARG236 |
| site_id | CC5 |
| Number of Residues | 2 |
| Details | BINDING SITE FOR RESIDUE SO4 C 603 |
| Chain | Residue |
| C | TRP139 |
| C | SER415 |
| site_id | CC6 |
| Number of Residues | 4 |
| Details | BINDING SITE FOR RESIDUE SO4 C 604 |
| Chain | Residue |
| C | SER131 |
| C | GLU132 |
| C | ARG133 |
| C | LEU134 |
| site_id | CC7 |
| Number of Residues | 5 |
| Details | BINDING SITE FOR RESIDUE SO4 C 605 |
| Chain | Residue |
| C | ASP95 |
| C | THR97 |
| C | ASP102 |
| C | HIS282 |
| C | HOH2030 |
| site_id | CC8 |
| Number of Residues | 3 |
| Details | BINDING SITE FOR RESIDUE CO C 610 |
| Chain | Residue |
| C | GLU188 |
| C | HIS247 |
| C | GLU251 |
| site_id | CC9 |
| Number of Residues | 2 |
| Details | BINDING SITE FOR RESIDUE CO C 612 |
| Chain | Residue |
| C | LEU63 |
| C | HIS67 |
| site_id | DC1 |
| Number of Residues | 3 |
| Details | BINDING SITE FOR RESIDUE CO C 613 |
| Chain | Residue |
| C | HIS158 |
| C | GLU168 |
| C | HOH2148 |
| site_id | DC2 |
| Number of Residues | 8 |
| Details | BINDING SITE FOR RESIDUE BIY D 500 |
| Chain | Residue |
| D | SER49 |
| D | TYR147 |
| D | SER298 |
| D | ASN300 |
| D | GLY412 |
| D | THR413 |
| D | HOH2124 |
| D | ALA48 |
| site_id | DC3 |
| Number of Residues | 2 |
| Details | BINDING SITE FOR RESIDUE SO4 D 601 |
| Chain | Residue |
| D | HIS282 |
| D | THR283 |
| site_id | DC4 |
| Number of Residues | 2 |
| Details | BINDING SITE FOR RESIDUE SO4 D 602 |
| Chain | Residue |
| D | ALA234 |
| D | ARG236 |
| site_id | DC5 |
| Number of Residues | 2 |
| Details | BINDING SITE FOR RESIDUE SO4 D 603 |
| Chain | Residue |
| D | GLU141 |
| D | ASP211 |
| site_id | DC6 |
| Number of Residues | 4 |
| Details | BINDING SITE FOR RESIDUE SO4 D 604 |
| Chain | Residue |
| D | SER131 |
| D | GLU132 |
| D | ARG133 |
| D | LEU134 |
| site_id | DC7 |
| Number of Residues | 5 |
| Details | BINDING SITE FOR RESIDUE SO4 D 605 |
| Chain | Residue |
| D | ASP95 |
| D | THR97 |
| D | ASP102 |
| D | HIS282 |
| D | HOH2024 |
| site_id | DC8 |
| Number of Residues | 4 |
| Details | BINDING SITE FOR RESIDUE CO D 610 |
| Chain | Residue |
| D | GLU188 |
| D | HIS247 |
| D | GLU251 |
| D | HOH2137 |
| site_id | DC9 |
| Number of Residues | 1 |
| Details | BINDING SITE FOR RESIDUE CO D 611 |
| Chain | Residue |
| D | HIS462 |
| site_id | EC1 |
| Number of Residues | 2 |
| Details | BINDING SITE FOR RESIDUE CO D 612 |
| Chain | Residue |
| D | LEU63 |
| D | HIS67 |
| site_id | EC2 |
| Number of Residues | 3 |
| Details | BINDING SITE FOR RESIDUE CO D 613 |
| Chain | Residue |
| D | HIS158 |
| D | GLU168 |
| D | HOH2138 |
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 |
