2VGK
Crystal structure of Actinomadura R39 DD-peptidase complexed with a peptidoglycan-mimetic cephalosporin
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 | 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 | 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 | 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 | 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 | 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 | 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 | 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 | 10 |
Details | BINDING SITE FOR RESIDUE REZ A 500 |
Chain | Residue |
A | TRP139 |
B | GLU176 |
A | ASP142 |
A | TYR147 |
A | ARG351 |
A | SER415 |
A | SO4600 |
A | HOH2109 |
A | HOH2110 |
A | HOH2111 |
site_id | AC2 |
Number of Residues | 7 |
Details | BINDING SITE FOR RESIDUE SO4 A 600 |
Chain | Residue |
A | SER49 |
A | SER298 |
A | LYS410 |
A | THR411 |
A | GLY412 |
A | THR413 |
A | REZ500 |
site_id | AC3 |
Number of Residues | 3 |
Details | BINDING SITE FOR RESIDUE SO4 A 601 |
Chain | Residue |
A | HIS282 |
A | THR283 |
A | HOH2112 |
site_id | AC4 |
Number of Residues | 4 |
Details | BINDING SITE FOR RESIDUE SO4 A 602 |
Chain | Residue |
A | ALA234 |
A | ARG236 |
A | HOH2113 |
B | HOH2056 |
site_id | AC5 |
Number of Residues | 2 |
Details | BINDING SITE FOR RESIDUE SO4 A 603 |
Chain | Residue |
A | ARG133 |
A | LEU134 |
site_id | AC6 |
Number of Residues | 4 |
Details | BINDING SITE FOR RESIDUE SO4 A 604 |
Chain | Residue |
A | GLY159 |
A | GLU160 |
A | ARG161 |
A | HOH2115 |
site_id | AC7 |
Number of Residues | 3 |
Details | BINDING SITE FOR RESIDUE MG A 610 |
Chain | Residue |
A | GLU188 |
A | HIS247 |
A | GLU251 |
site_id | AC8 |
Number of Residues | 2 |
Details | BINDING SITE FOR RESIDUE MG A 611 |
Chain | Residue |
A | VAL406 |
A | HIS462 |
site_id | AC9 |
Number of Residues | 11 |
Details | BINDING SITE FOR RESIDUE REZ B 500 |
Chain | Residue |
B | TRP139 |
B | ASP142 |
B | TYR147 |
B | SER298 |
B | ASN300 |
B | ARG351 |
B | MET414 |
B | SER415 |
B | SO4600 |
B | HOH2109 |
B | HOH2110 |
site_id | BC1 |
Number of Residues | 7 |
Details | BINDING SITE FOR RESIDUE SO4 B 600 |
Chain | Residue |
B | SER49 |
B | SER298 |
B | THR411 |
B | GLY412 |
B | THR413 |
B | REZ500 |
B | HOH2009 |
site_id | BC2 |
Number of Residues | 3 |
Details | BINDING SITE FOR RESIDUE SO4 B 601 |
Chain | Residue |
B | ASP281 |
B | HIS282 |
B | THR283 |
site_id | BC3 |
Number of Residues | 3 |
Details | BINDING SITE FOR RESIDUE SO4 B 602 |
Chain | Residue |
B | ALA234 |
B | ARG236 |
B | HOH2111 |
site_id | BC4 |
Number of Residues | 3 |
Details | BINDING SITE FOR RESIDUE SO4 B 603 |
Chain | Residue |
B | GLU132 |
B | ARG133 |
B | LEU134 |
site_id | BC5 |
Number of Residues | 3 |
Details | BINDING SITE FOR RESIDUE SO4 B 604 |
Chain | Residue |
B | GLY159 |
B | GLU160 |
B | ARG161 |
site_id | BC6 |
Number of Residues | 10 |
Details | BINDING SITE FOR RESIDUE REZ C 500 |
Chain | Residue |
C | ASP142 |
C | TYR147 |
C | SER298 |
C | ASN300 |
C | ARG351 |
C | MET414 |
C | SER415 |
C | SO4600 |
C | HOH2014 |
C | HOH2105 |
site_id | BC7 |
Number of Residues | 8 |
Details | BINDING SITE FOR RESIDUE SO4 C 600 |
Chain | Residue |
C | SER49 |
C | SER298 |
C | LYS410 |
C | THR411 |
C | GLY412 |
C | THR413 |
C | REZ500 |
C | HOH2122 |
site_id | BC8 |
Number of Residues | 4 |
Details | BINDING SITE FOR RESIDUE SO4 C 601 |
Chain | Residue |
C | ASP281 |
C | HIS282 |
C | THR283 |
C | HOH2123 |
site_id | BC9 |
Number of Residues | 2 |
Details | BINDING SITE FOR RESIDUE SO4 C 602 |
Chain | Residue |
C | ALA234 |
C | ARG236 |
site_id | CC1 |
Number of Residues | 2 |
Details | BINDING SITE FOR RESIDUE SO4 C 603 |
Chain | Residue |
C | ARG133 |
C | LEU134 |
site_id | CC2 |
Number of Residues | 3 |
Details | BINDING SITE FOR RESIDUE SO4 C 604 |
Chain | Residue |
C | GLY159 |
C | GLU160 |
C | ARG161 |
site_id | CC3 |
Number of Residues | 8 |
Details | BINDING SITE FOR RESIDUE SO4 D 600 |
Chain | Residue |
D | THR413 |
D | HOH2017 |
D | HOH2146 |
D | SER49 |
D | SER298 |
D | LYS410 |
D | THR411 |
D | GLY412 |
site_id | CC4 |
Number of Residues | 2 |
Details | BINDING SITE FOR RESIDUE SO4 D 601 |
Chain | Residue |
D | HIS282 |
D | THR283 |
site_id | CC5 |
Number of Residues | 2 |
Details | BINDING SITE FOR RESIDUE SO4 D 602 |
Chain | Residue |
D | ALA234 |
D | ARG236 |
site_id | CC6 |
Number of Residues | 4 |
Details | BINDING SITE FOR RESIDUE SO4 D 603 |
Chain | Residue |
D | SER131 |
D | GLU132 |
D | ARG133 |
D | LEU134 |
site_id | CC7 |
Number of Residues | 3 |
Details | BINDING SITE FOR RESIDUE SO4 D 604 |
Chain | Residue |
D | GLY159 |
D | GLU160 |
D | ARG161 |
site_id | CC8 |
Number of Residues | 3 |
Details | BINDING SITE FOR RESIDUE MG D 610 |
Chain | Residue |
D | GLU188 |
D | HIS247 |
D | GLU251 |
site_id | CC9 |
Number of Residues | 1 |
Details | BINDING SITE FOR RESIDUE MG D 611 |
Chain | Residue |
D | HIS462 |
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 |