5MC3
Crystal Structure of Glu412Lys 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 | 6 |
| Details | binding site for residue MN A 500 |
| Chain | Residue |
| A | ASP276 |
| A | ASP287 |
| A | LYS412 |
| A | GLU452 |
| A | OH501 |
| A | GLY503 |
| site_id | AC2 |
| Number of Residues | 7 |
| Details | binding site for residue OH A 501 |
| Chain | Residue |
| A | GLU452 |
| A | MN500 |
| A | GLY503 |
| A | PRO504 |
| A | ASP276 |
| A | LYS412 |
| A | ARG450 |
| site_id | AC3 |
| Number of Residues | 11 |
| Details | binding site for residue GLY A 503 |
| Chain | Residue |
| A | TYR241 |
| A | ILE244 |
| A | HIS255 |
| A | ASP276 |
| A | ASP287 |
| A | HIS377 |
| A | LYS412 |
| A | MN500 |
| A | OH501 |
| A | PRO504 |
| A | HOH757 |
| site_id | AC4 |
| Number of Residues | 11 |
| Details | binding site for residue PRO A 504 |
| Chain | Residue |
| A | LEU254 |
| A | HIS255 |
| A | HIS366 |
| A | HIS377 |
| A | ARG398 |
| A | ARG450 |
| A | OH501 |
| A | GLY503 |
| A | HOH759 |
| A | HOH792 |
| B | TRP107 |
| site_id | AC5 |
| Number of Residues | 4 |
| Details | binding site for residue NA A 505 |
| Chain | Residue |
| A | GLY235 |
| A | TYR282 |
| A | HOH648 |
| A | HOH690 |
| site_id | AC6 |
| Number of Residues | 8 |
| Details | binding site for residue GOL A 506 |
| Chain | Residue |
| A | PHE9 |
| A | TRP10 |
| A | LEU11 |
| A | LYS120 |
| A | HOH608 |
| A | HOH626 |
| A | HOH681 |
| B | ASP264 |
| site_id | AC7 |
| Number of Residues | 5 |
| Details | binding site for residue GOL A 507 |
| Chain | Residue |
| A | GLY109 |
| A | LYS110 |
| A | HOH601 |
| A | HOH917 |
| B | HOH661 |
| site_id | AC8 |
| Number of Residues | 3 |
| Details | binding site for residue GOL A 508 |
| Chain | Residue |
| A | ASP390 |
| A | PRO392 |
| A | ARG395 |
| site_id | AC9 |
| Number of Residues | 3 |
| Details | binding site for residue GOL A 509 |
| Chain | Residue |
| A | GLU387 |
| A | ARG388 |
| A | HOH761 |
| site_id | AD1 |
| Number of Residues | 6 |
| Details | binding site for residue MN B 500 |
| Chain | Residue |
| B | ASP276 |
| B | ASP287 |
| B | LYS412 |
| B | GLU452 |
| B | OH501 |
| B | GLY503 |
| site_id | AD2 |
| Number of Residues | 7 |
| Details | binding site for residue OH B 501 |
| Chain | Residue |
| B | ASP276 |
| B | LYS412 |
| B | ARG450 |
| B | GLU452 |
| B | MN500 |
| B | GLY503 |
| B | PRO504 |
| site_id | AD3 |
| Number of Residues | 11 |
| Details | binding site for residue GLY B 503 |
| Chain | Residue |
| B | TYR241 |
| B | ILE244 |
| B | HIS255 |
| B | ASP276 |
| B | ASP287 |
| B | HIS377 |
| B | LYS412 |
| B | MN500 |
| B | OH501 |
| B | PRO504 |
| B | HOH637 |
| site_id | AD4 |
| Number of Residues | 12 |
| Details | binding site for residue PRO B 504 |
| Chain | Residue |
| A | TRP107 |
| B | LEU254 |
| B | HIS255 |
| B | HIS366 |
| B | HIS377 |
| B | ARG398 |
| B | LYS412 |
| B | ARG450 |
| B | OH501 |
| B | GLY503 |
| B | HOH778 |
| B | HOH782 |
| site_id | AD5 |
| Number of Residues | 7 |
| Details | binding site for residue NA B 505 |
| Chain | Residue |
| B | HOH986 |
| B | HOH997 |
| B | LYS211 |
| B | MET479 |
| B | GOL507 |
| B | HOH752 |
| B | HOH948 |
| site_id | AD6 |
| Number of Residues | 6 |
| Details | binding site for residue GOL B 506 |
| Chain | Residue |
| A | ARG311 |
| A | HOH845 |
| A | HOH1033 |
| B | ARG35 |
| B | ALA42 |
| B | ASP89 |
| site_id | AD7 |
| Number of Residues | 12 |
| Details | binding site for residue GOL B 507 |
| Chain | Residue |
| A | PRO429 |
| B | VAL213 |
| B | LYS214 |
| B | VAL215 |
| B | ALA294 |
| B | ASN295 |
| B | MET479 |
| B | NA505 |
| B | HOH611 |
| B | HOH752 |
| B | HOH852 |
| B | HOH948 |
| site_id | AD8 |
| Number of Residues | 5 |
| Details | binding site for residue GOL B 508 |
| Chain | Residue |
| B | SER134 |
| B | SER138 |
| B | SER350 |
| B | VAL351 |
| B | ASP352 |
| site_id | AD9 |
| Number of Residues | 6 |
| Details | binding site for residue GOL B 509 |
| Chain | Residue |
| B | GLY270 |
| B | ARG442 |
| B | ARG444 |
| B | PHE446 |
| B | HOH671 |
| B | HOH863 |
| site_id | AE1 |
| Number of Residues | 4 |
| Details | binding site for residue GOL B 510 |
| Chain | Residue |
| B | LYS187 |
| B | ASP189 |
| B | GLY406 |
| B | VAL457 |
| site_id | AE2 |
| Number of Residues | 4 |
| Details | binding site for residue GOL B 511 |
| Chain | Residue |
| B | THR152 |
| B | GLU387 |
| B | ARG388 |
| B | HOH646 |
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 | HIS366-ASP378 |
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 | HIS255 | |
| A | HIS377 | |
| A | ARG398 | |
| B | HIS255 | |
| B | HIS377 | |
| B | ARG398 |
| 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 | ASP276 | |
| B | GLU452 | |
| A | ASP287 | |
| A | HIS370 | |
| A | LYS412 | |
| A | GLU452 | |
| B | ASP276 | |
| B | ASP287 | |
| B | HIS370 | |
| B | LYS412 |
| site_id | SWS_FT_FI3 |
| Number of Residues | 2 |
| Details | MOD_RES: Phosphoserine => ECO:0007744|PubMed:24275569 |
| Chain | Residue | Details |
| A | SER167 | |
| B | SER167 |
