5MC0
Crystal Structure of delTyr231 mutant of Human Prolidase with Mn ions and GlyPro ligand
Functional Information from GO Data
| Chain | GOid | namespace | contents |
| A | 0004181 | molecular_function | metallocarboxypeptidase activity |
| A | 0005515 | molecular_function | protein binding |
| A | 0006508 | biological_process | proteolysis |
| A | 0006520 | biological_process | amino acid metabolic process |
| A | 0008233 | molecular_function | peptidase activity |
| A | 0008237 | molecular_function | metallopeptidase activity |
| A | 0016805 | molecular_function | dipeptidase activity |
| A | 0030145 | molecular_function | manganese ion binding |
| A | 0030574 | biological_process | collagen catabolic process |
| A | 0043069 | biological_process | negative regulation of programmed cell death |
| A | 0046872 | molecular_function | metal ion binding |
| A | 0070006 | molecular_function | metalloaminopeptidase activity |
| A | 0070062 | cellular_component | extracellular exosome |
| A | 0102009 | molecular_function | proline dipeptidase activity |
| B | 0004181 | molecular_function | metallocarboxypeptidase activity |
| B | 0005515 | molecular_function | protein binding |
| B | 0006508 | biological_process | proteolysis |
| B | 0006520 | biological_process | amino acid metabolic process |
| B | 0008233 | molecular_function | peptidase activity |
| B | 0008237 | molecular_function | metallopeptidase activity |
| B | 0016805 | molecular_function | dipeptidase activity |
| B | 0030145 | molecular_function | manganese ion binding |
| B | 0030574 | biological_process | collagen catabolic process |
| B | 0043069 | biological_process | negative regulation of programmed cell death |
| B | 0046872 | molecular_function | metal ion binding |
| B | 0070006 | molecular_function | metalloaminopeptidase activity |
| B | 0070062 | cellular_component | extracellular exosome |
| B | 0102009 | molecular_function | proline dipeptidase activity |
Functional Information from PDB Data
| site_id | AC1 |
| Number of Residues | 7 |
| Details | binding site for residue MN A 499 |
| Chain | Residue |
| A | ASP286 |
| A | HIS369 |
| A | GLU411 |
| A | GLU451 |
| A | MN500 |
| A | OH501 |
| A | GLY503 |
| site_id | AC2 |
| Number of Residues | 7 |
| Details | binding site for residue MN A 500 |
| Chain | Residue |
| A | THR288 |
| A | GLU451 |
| A | MN499 |
| A | OH501 |
| A | GLY503 |
| A | ASP275 |
| A | ASP286 |
| site_id | AC3 |
| Number of Residues | 8 |
| Details | binding site for residue OH A 501 |
| Chain | Residue |
| A | ASP275 |
| A | ASP286 |
| A | GLU411 |
| A | GLU451 |
| A | MN499 |
| A | MN500 |
| A | GLY503 |
| A | PRO504 |
| site_id | AC4 |
| Number of Residues | 10 |
| Details | binding site for residue GLY A 503 |
| Chain | Residue |
| A | TYR240 |
| A | ASP275 |
| A | ASP286 |
| A | HIS369 |
| A | HIS376 |
| A | MN499 |
| A | MN500 |
| A | OH501 |
| A | PRO504 |
| A | HOH648 |
| site_id | AC5 |
| Number of Residues | 11 |
| Details | binding site for residue PRO A 504 |
| Chain | Residue |
| A | HIS254 |
| A | HIS365 |
| A | HIS376 |
| A | ARG397 |
| A | GLU411 |
| A | ARG449 |
| A | OH501 |
| A | GLY503 |
| A | HOH764 |
| A | HOH824 |
| B | TRP107 |
| site_id | AC6 |
| Number of Residues | 8 |
| Details | binding site for residue GOL A 506 |
| Chain | Residue |
| A | TRP10 |
| A | LEU11 |
| A | LYS120 |
| A | HOH609 |
| A | HOH619 |
| A | HOH720 |
| A | HOH828 |
| B | ASP263 |
| site_id | AC7 |
| Number of Residues | 4 |
| Details | binding site for residue GOL A 507 |
| Chain | Residue |
| A | THR152 |
| A | GLU386 |
| A | ARG387 |
| A | HOH921 |
| site_id | AC8 |
| Number of Residues | 4 |
| Details | binding site for residue GOL A 508 |
| Chain | Residue |
| A | GLY384 |
| A | GLU386 |
| A | ALA399 |
| A | HOH655 |
| site_id | AC9 |
| Number of Residues | 7 |
| Details | binding site for residue GOL A 509 |
| Chain | Residue |
| A | ARG29 |
| A | ARG33 |
| A | LYS36 |
| A | GLU182 |
| A | PHE186 |
| A | HOH607 |
| A | HOH1016 |
| site_id | AD1 |
| Number of Residues | 5 |
| Details | binding site for residue GOL A 510 |
| Chain | Residue |
| A | PRO141 |
| A | LYS168 |
| A | PHE169 |
| A | HOH836 |
| A | HOH851 |
| site_id | AD2 |
| Number of Residues | 6 |
| Details | binding site for residue NA A 511 |
| Chain | Residue |
| A | GLY317 |
| A | HOH700 |
| A | HOH708 |
| A | HOH1036 |
| A | HOH1144 |
| B | ALA39 |
| site_id | AD3 |
| Number of Residues | 7 |
| Details | binding site for residue MN B 499 |
| Chain | Residue |
| B | ASP286 |
| B | HIS369 |
| B | GLU411 |
| B | GLU451 |
| B | MN500 |
| B | OH501 |
| B | GLY503 |
| site_id | AD4 |
| Number of Residues | 7 |
| Details | binding site for residue MN B 500 |
| Chain | Residue |
| B | ASP275 |
| B | ASP286 |
| B | THR288 |
| B | GLU451 |
| B | MN499 |
| B | OH501 |
| B | GLY503 |
| site_id | AD5 |
| Number of Residues | 8 |
| Details | binding site for residue OH B 501 |
| Chain | Residue |
| B | ASP275 |
| B | ASP286 |
| B | GLU411 |
| B | GLU451 |
| B | MN499 |
| B | MN500 |
| B | GLY503 |
| B | PRO504 |
| site_id | AD6 |
| Number of Residues | 10 |
| Details | binding site for residue GLY B 503 |
| Chain | Residue |
| B | TYR240 |
| B | ASP275 |
| B | ASP286 |
| B | HIS369 |
| B | HIS376 |
| B | MN499 |
| B | MN500 |
| B | OH501 |
| B | PRO504 |
| B | HOH778 |
| site_id | AD7 |
| Number of Residues | 10 |
| Details | binding site for residue PRO B 504 |
| Chain | Residue |
| B | HIS254 |
| B | HIS365 |
| B | HIS376 |
| B | ARG397 |
| B | GLU411 |
| B | ARG449 |
| B | OH501 |
| B | GLY503 |
| B | HOH743 |
| B | HOH900 |
| site_id | AD8 |
| Number of Residues | 3 |
| Details | binding site for residue CL B 506 |
| Chain | Residue |
| B | ARG436 |
| B | GLN440 |
| B | ARG443 |
| site_id | AD9 |
| Number of Residues | 8 |
| Details | binding site for residue GOL B 507 |
| Chain | Residue |
| A | ASP263 |
| B | PHE9 |
| B | TRP10 |
| B | LEU11 |
| B | HOH622 |
| B | HOH645 |
| B | HOH722 |
| B | HOH785 |
| site_id | AE1 |
| Number of Residues | 5 |
| Details | binding site for residue GOL B 508 |
| Chain | Residue |
| B | GLU14 |
| B | TYR197 |
| B | LYS200 |
| B | HOH637 |
| B | HOH641 |
| site_id | AE2 |
| Number of Residues | 6 |
| Details | binding site for residue GOL B 509 |
| Chain | Residue |
| B | SER134 |
| B | SER138 |
| B | GLY348 |
| B | SER349 |
| B | VAL350 |
| B | ASP351 |
| site_id | AE3 |
| Number of Residues | 4 |
| Details | binding site for residue GOL B 510 |
| Chain | Residue |
| B | GLU386 |
| B | ARG387 |
| B | HOH834 |
| B | HOH848 |
| site_id | AE4 |
| Number of Residues | 6 |
| Details | binding site for residue GOL B 511 |
| Chain | Residue |
| B | PHE163 |
| B | ASP164 |
| B | GLY165 |
| B | ILE166 |
| B | SER167 |
| B | HOH625 |
| site_id | AE5 |
| Number of Residues | 6 |
| Details | binding site for residue GOL B 512 |
| Chain | Residue |
| B | TYR83 |
| B | VAL129 |
| B | PHE163 |
| B | ASP164 |
| B | HOH617 |
| B | HOH991 |
| site_id | AE6 |
| Number of Residues | 4 |
| Details | binding site for residue GOL B 513 |
| Chain | Residue |
| B | LYS168 |
| B | HOH602 |
| B | HOH609 |
| B | HOH614 |
| site_id | AE7 |
| Number of Residues | 2 |
| Details | binding site for residue GOL B 514 |
| Chain | Residue |
| A | HIS228 |
| B | HIS228 |
| site_id | AE8 |
| Number of Residues | 7 |
| Details | binding site for residue NA B 515 |
| Chain | Residue |
| B | MET210 |
| B | LYS211 |
| B | VAL213 |
| B | MET478 |
| B | HOH611 |
| B | HOH1057 |
| B | HOH1100 |
Functional Information from PROSITE/UniProt
| site_id | PS00491 |
| Number of Residues | 13 |
| Details | PROLINE_PEPTIDASE Aminopeptidase P and proline dipeptidase signature. HGLGHfLGIdVHD |
| Chain | Residue | Details |
| A | HIS365-ASP377 |
Functional Information from SwissProt/UniProt
| site_id | SWS_FT_FI1 |
| Number of Residues | 6 |
| Details | BINDING: BINDING => ECO:0000269|PubMed:28677335, ECO:0007744|PDB:5M4J, ECO:0007744|PDB:5M4L |
| Chain | Residue | Details |
| A | TYR255 | |
| A | ASP377 | |
| A | THR398 | |
| B | TYR255 | |
| B | ASP377 | |
| B | THR398 |
| site_id | SWS_FT_FI2 |
| Number of Residues | 10 |
| Details | BINDING: BINDING => ECO:0000269|PubMed:28677335, ECO:0007744|PDB:5M4G, ECO:0007744|PDB:5M4L, ECO:0007744|PDB:5M4Q |
| Chain | Residue | Details |
| A | MET276 | |
| B | GLU452 | |
| A | ILE287 | |
| A | PHE370 | |
| A | PRO412 | |
| A | GLU452 | |
| B | MET276 | |
| B | ILE287 | |
| B | PHE370 | |
| B | PRO412 |
| site_id | SWS_FT_FI3 |
| Number of Residues | 2 |
| Details | MOD_RES: Phosphoserine => ECO:0007744|PubMed:24275569 |
| Chain | Residue | Details |
| A | SER167 | |
| B | SER167 |
