5M4Q
Crystal Structure of Wild-Type Human Prolidase with Mn ions and Pro 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 | 0008235 | molecular_function | metalloexopeptidase activity |
| A | 0008237 | molecular_function | metallopeptidase activity |
| A | 0016787 | molecular_function | hydrolase 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 | 0008235 | molecular_function | metalloexopeptidase activity |
| B | 0008237 | molecular_function | metallopeptidase activity |
| B | 0016787 | molecular_function | hydrolase 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 | ASP287 |
| A | HIS370 |
| A | GLU412 |
| A | GLU452 |
| A | MN500 |
| A | OH501 |
| A | HOH619 |
| site_id | AC2 |
| Number of Residues | 7 |
| Details | binding site for residue MN A 500 |
| Chain | Residue |
| A | THR289 |
| A | GLU452 |
| A | MN499 |
| A | OH501 |
| A | HOH877 |
| A | ASP276 |
| A | ASP287 |
| site_id | AC3 |
| Number of Residues | 9 |
| Details | binding site for residue OH A 501 |
| Chain | Residue |
| A | ASP276 |
| A | ASP287 |
| A | GLU412 |
| A | GLU452 |
| A | MN499 |
| A | MN500 |
| A | PRO504 |
| A | HOH619 |
| A | HOH877 |
| site_id | AC4 |
| Number of Residues | 10 |
| Details | binding site for residue PRO A 504 |
| Chain | Residue |
| A | HIS255 |
| A | HIS366 |
| A | HIS377 |
| A | ARG398 |
| A | GLU412 |
| A | OH501 |
| A | HOH619 |
| A | HOH702 |
| A | HOH734 |
| B | TRP107 |
| site_id | AC5 |
| Number of Residues | 5 |
| Details | binding site for residue GOL A 505 |
| Chain | Residue |
| A | PHE9 |
| A | TRP10 |
| A | HOH603 |
| A | HOH621 |
| B | ASP264 |
| site_id | AC6 |
| Number of Residues | 9 |
| Details | binding site for residue GOL A 506 |
| Chain | Residue |
| A | HIS330 |
| A | ARG331 |
| A | ASP334 |
| A | HIS358 |
| A | GLU391 |
| A | PRO392 |
| A | LEU394 |
| A | HOH602 |
| A | HOH605 |
| site_id | AC7 |
| Number of Residues | 4 |
| Details | binding site for residue GOL A 507 |
| Chain | Residue |
| A | THR152 |
| A | GLU387 |
| A | ARG388 |
| A | HOH715 |
| site_id | AC8 |
| Number of Residues | 5 |
| Details | binding site for residue GOL A 508 |
| Chain | Residue |
| A | ALA342 |
| A | HIS343 |
| A | LEU347 |
| A | SER348 |
| A | HOH676 |
| site_id | AC9 |
| Number of Residues | 7 |
| Details | binding site for residue MN B 499 |
| Chain | Residue |
| B | ASP287 |
| B | HIS370 |
| B | GLU412 |
| B | GLU452 |
| B | MN500 |
| B | OH501 |
| B | HOH631 |
| site_id | AD1 |
| Number of Residues | 7 |
| Details | binding site for residue MN B 500 |
| Chain | Residue |
| B | ASP276 |
| B | ASP287 |
| B | THR289 |
| B | GLU452 |
| B | MN499 |
| B | OH501 |
| B | HOH871 |
| site_id | AD2 |
| Number of Residues | 9 |
| Details | binding site for residue OH B 501 |
| Chain | Residue |
| B | ASP276 |
| B | ASP287 |
| B | GLU412 |
| B | GLU452 |
| B | MN499 |
| B | MN500 |
| B | PRO504 |
| B | HOH631 |
| B | HOH871 |
| site_id | AD3 |
| Number of Residues | 10 |
| Details | binding site for residue PRO B 504 |
| Chain | Residue |
| A | TRP107 |
| B | HIS255 |
| B | HIS366 |
| B | HIS377 |
| B | ARG398 |
| B | GLU412 |
| B | OH501 |
| B | HOH631 |
| B | HOH754 |
| B | HOH800 |
| site_id | AD4 |
| Number of Residues | 9 |
| Details | binding site for residue GOL B 505 |
| Chain | Residue |
| A | ASP264 |
| B | PHE9 |
| B | TRP10 |
| B | LEU11 |
| B | LYS120 |
| B | HOH674 |
| B | HOH752 |
| B | HOH757 |
| B | HOH965 |
| site_id | AD5 |
| Number of Residues | 5 |
| Details | binding site for residue GOL B 506 |
| Chain | Residue |
| B | GLY165 |
| B | ILE166 |
| B | SER167 |
| B | HOH662 |
| B | ASP164 |
| site_id | AD6 |
| Number of Residues | 10 |
| Details | binding site for residue GOL B 507 |
| Chain | Residue |
| A | GLU227 |
| A | HIS228 |
| A | TYR231 |
| A | HOH895 |
| B | SER224 |
| B | GLU227 |
| B | HIS228 |
| B | HOH632 |
| B | HOH819 |
| B | HOH834 |
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 site: {"evidences":[{"source":"PubMed","id":"28677335","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"5M4J","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"5M4L","evidenceCode":"ECO:0007744"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI2 |
| Number of Residues | 10 |
| Details | Binding site: {"evidences":[{"source":"PubMed","id":"28677335","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"5M4G","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"5M4L","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"5M4Q","evidenceCode":"ECO:0007744"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI3 |
| Number of Residues | 2 |
| Details | Modified residue: {"description":"Phosphoserine","evidences":[{"source":"PubMed","id":"24275569","evidenceCode":"ECO:0007744"}]} |
| Chain | Residue | Details |
