1W8Y
Crystal structure of the nitrocefin acyl-DD-peptidase from Actinomadura R39.
Functional Information from GO Data
| Chain | GOid | namespace | contents |
| A | 0000270 | biological_process | peptidoglycan metabolic process |
| A | 0004185 | molecular_function | serine-type carboxypeptidase activity |
| A | 0005576 | cellular_component | extracellular region |
| A | 0006508 | biological_process | proteolysis |
| A | 0009002 | molecular_function | serine-type D-Ala-D-Ala carboxypeptidase activity |
| A | 0009252 | biological_process | peptidoglycan biosynthetic process |
| B | 0000270 | biological_process | peptidoglycan metabolic process |
| B | 0004185 | molecular_function | serine-type carboxypeptidase activity |
| B | 0005576 | cellular_component | extracellular region |
| B | 0006508 | biological_process | proteolysis |
| B | 0009002 | molecular_function | serine-type D-Ala-D-Ala carboxypeptidase activity |
| B | 0009252 | biological_process | peptidoglycan biosynthetic process |
| C | 0000270 | biological_process | peptidoglycan metabolic process |
| C | 0004185 | molecular_function | serine-type carboxypeptidase activity |
| C | 0005576 | cellular_component | extracellular region |
| C | 0006508 | biological_process | proteolysis |
| C | 0009002 | molecular_function | serine-type D-Ala-D-Ala carboxypeptidase activity |
| C | 0009252 | biological_process | peptidoglycan biosynthetic process |
| D | 0000270 | biological_process | peptidoglycan metabolic process |
| D | 0004185 | molecular_function | serine-type carboxypeptidase activity |
| D | 0005576 | cellular_component | extracellular region |
| D | 0006508 | biological_process | proteolysis |
| D | 0009002 | molecular_function | serine-type D-Ala-D-Ala carboxypeptidase activity |
| D | 0009252 | biological_process | peptidoglycan biosynthetic process |
Functional Information from PDB Data
| site_id | AC1 |
| Number of Residues | 4 |
| Details | BINDING SITE FOR RESIDUE SO4 A 501 |
| Chain | Residue |
| A | ASP281 |
| A | HIS282 |
| A | THR283 |
| A | HOH2186 |
| site_id | AC2 |
| Number of Residues | 2 |
| Details | BINDING SITE FOR RESIDUE SO4 A 502 |
| Chain | Residue |
| A | ALA234 |
| A | ARG236 |
| site_id | AC3 |
| Number of Residues | 4 |
| Details | BINDING SITE FOR RESIDUE SO4 A 503 |
| Chain | Residue |
| A | HOH2048 |
| A | GLU132 |
| A | ARG133 |
| A | LEU134 |
| site_id | AC4 |
| Number of Residues | 7 |
| Details | BINDING SITE FOR RESIDUE SO4 A 504 |
| Chain | Residue |
| A | GLY159 |
| A | GLU160 |
| A | ARG161 |
| A | HOH2072 |
| A | HOH2188 |
| A | HOH2189 |
| A | HOH2190 |
| site_id | AC5 |
| Number of Residues | 4 |
| Details | BINDING SITE FOR RESIDUE MG A 510 |
| Chain | Residue |
| A | ALA186 |
| A | GLU188 |
| A | HIS247 |
| A | GLU251 |
| site_id | AC6 |
| Number of Residues | 2 |
| Details | BINDING SITE FOR RESIDUE MG A 511 |
| Chain | Residue |
| A | VAL406 |
| A | HIS462 |
| site_id | AC7 |
| Number of Residues | 5 |
| Details | BINDING SITE FOR RESIDUE SO4 B 501 |
| Chain | Residue |
| B | ASP281 |
| B | HIS282 |
| B | THR283 |
| B | HOH2216 |
| B | HOH2217 |
| site_id | AC8 |
| Number of Residues | 3 |
| Details | BINDING SITE FOR RESIDUE SO4 B 502 |
| Chain | Residue |
| B | ALA234 |
| B | ARG236 |
| B | HOH2219 |
| site_id | AC9 |
| Number of Residues | 4 |
| Details | BINDING SITE FOR RESIDUE SO4 B 503 |
| Chain | Residue |
| B | SER131 |
| B | GLU132 |
| B | ARG133 |
| B | LEU134 |
| site_id | BC1 |
| Number of Residues | 4 |
| Details | BINDING SITE FOR RESIDUE SO4 B 504 |
| Chain | Residue |
| B | GLY159 |
| B | GLU160 |
| B | ARG161 |
| B | HOH2222 |
| site_id | BC2 |
| Number of Residues | 5 |
| Details | BINDING SITE FOR RESIDUE SO4 C 501 |
| Chain | Residue |
| C | ASP281 |
| C | HIS282 |
| C | THR283 |
| C | HOH2192 |
| C | HOH2193 |
| site_id | BC3 |
| Number of Residues | 3 |
| Details | BINDING SITE FOR RESIDUE SO4 C 502 |
| Chain | Residue |
| C | ARG236 |
| C | HOH2133 |
| C | HOH2194 |
| site_id | BC4 |
| Number of Residues | 4 |
| Details | BINDING SITE FOR RESIDUE SO4 C 503 |
| Chain | Residue |
| C | SER131 |
| C | ARG133 |
| C | LEU134 |
| C | HOH2063 |
| site_id | BC5 |
| Number of Residues | 6 |
| Details | BINDING SITE FOR RESIDUE SO4 C 504 |
| Chain | Residue |
| C | HIS158 |
| C | GLY159 |
| C | GLU160 |
| C | ARG161 |
| C | HOH2197 |
| C | HOH2198 |
| site_id | BC6 |
| Number of Residues | 5 |
| Details | BINDING SITE FOR RESIDUE SO4 D 501 |
| Chain | Residue |
| D | HIS282 |
| D | THR283 |
| D | HOH2132 |
| D | HOH2211 |
| D | HOH2212 |
| site_id | BC7 |
| Number of Residues | 4 |
| Details | BINDING SITE FOR RESIDUE SO4 D 502 |
| Chain | Residue |
| D | ALA234 |
| D | ARG236 |
| D | HOH2213 |
| D | HOH2214 |
| site_id | BC8 |
| Number of Residues | 5 |
| Details | BINDING SITE FOR RESIDUE SO4 D 503 |
| Chain | Residue |
| D | SER131 |
| D | GLU132 |
| D | ARG133 |
| D | LEU134 |
| D | HOH2215 |
| site_id | BC9 |
| Number of Residues | 5 |
| Details | BINDING SITE FOR RESIDUE SO4 D 504 |
| Chain | Residue |
| D | HIS158 |
| D | GLY159 |
| D | GLU160 |
| D | ARG161 |
| D | HOH2217 |
| site_id | CC1 |
| Number of Residues | 3 |
| Details | BINDING SITE FOR RESIDUE MG D 510 |
| Chain | Residue |
| D | GLU188 |
| D | HIS247 |
| D | GLU251 |
| site_id | CC2 |
| Number of Residues | 1 |
| Details | BINDING SITE FOR RESIDUE MG D 511 |
| Chain | Residue |
| D | HIS462 |
| site_id | CC3 |
| Number of Residues | 13 |
| Details | BINDING SITE FOR RESIDUE NCF A 520 |
| Chain | Residue |
| A | ALA48 |
| A | SER49 |
| A | TYR147 |
| A | SER298 |
| A | ASN300 |
| A | LEU349 |
| A | THR411 |
| A | GLY412 |
| A | THR413 |
| A | MET414 |
| A | HOH2191 |
| B | GLU176 |
| B | HOH2109 |
| site_id | CC4 |
| Number of Residues | 10 |
| Details | BINDING SITE FOR RESIDUE NCF B 520 |
| Chain | Residue |
| B | LYS410 |
| B | THR411 |
| B | GLY412 |
| B | THR413 |
| B | ALA48 |
| B | SER49 |
| B | TYR147 |
| B | SER298 |
| B | ASN300 |
| B | LEU349 |
| site_id | CC5 |
| Number of Residues | 8 |
| Details | BINDING SITE FOR RESIDUE NCF C 520 |
| Chain | Residue |
| C | ALA48 |
| C | SER49 |
| C | TYR147 |
| C | SER298 |
| C | ASN300 |
| C | THR411 |
| C | GLY412 |
| C | THR413 |
| site_id | CC6 |
| Number of Residues | 11 |
| Details | BINDING SITE FOR RESIDUE NCF D 520 |
| Chain | Residue |
| D | ALA48 |
| D | SER49 |
| D | ASP142 |
| D | TYR147 |
| D | SER298 |
| D | ASN300 |
| D | LEU349 |
| D | THR411 |
| D | GLY412 |
| D | THR413 |
| D | HOH2218 |
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 |
