5M4G
Crystal Structure of Wild-Type Human Prolidase with Mn ions
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 | ASP287 |
| A | HIS370 |
| A | GLU412 |
| A | GLU452 |
| A | MN500 |
| A | OH501 |
| A | HOH661 |
| 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 | HOH791 |
| A | ASP276 |
| A | ASP287 |
| site_id | AC3 |
| Number of Residues | 8 |
| Details | binding site for residue OH A 501 |
| Chain | Residue |
| A | ASP276 |
| A | GLU412 |
| A | GLU452 |
| A | MN499 |
| A | MN500 |
| A | HOH616 |
| A | HOH661 |
| A | HOH791 |
| site_id | AC4 |
| Number of Residues | 5 |
| Details | binding site for residue GOL A 504 |
| Chain | Residue |
| A | ASP164 |
| A | GLY165 |
| A | ILE166 |
| A | SER167 |
| A | HOH609 |
| site_id | AC5 |
| Number of Residues | 6 |
| Details | binding site for residue GOL A 505 |
| Chain | Residue |
| A | PHE9 |
| A | TRP10 |
| A | LYS120 |
| A | HOH610 |
| A | HOH754 |
| B | ASP264 |
| site_id | AC6 |
| Number of Residues | 8 |
| Details | binding site for residue GOL A 506 |
| Chain | Residue |
| A | TRP325 |
| A | PRO327 |
| A | ASP328 |
| A | ARG331 |
| A | GLU391 |
| A | LEU394 |
| A | HOH603 |
| A | HOH638 |
| site_id | AC7 |
| 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 | HOH652 |
| site_id | AC8 |
| 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 | HOH830 |
| site_id | AC9 |
| Number of Residues | 8 |
| Details | binding site for residue OH B 501 |
| Chain | Residue |
| B | ASP276 |
| B | ASP287 |
| B | GLU412 |
| B | GLU452 |
| B | MN499 |
| B | MN500 |
| B | HOH652 |
| B | HOH830 |
| site_id | AD1 |
| Number of Residues | 8 |
| Details | binding site for residue GOL B 504 |
| Chain | Residue |
| A | ASP264 |
| B | PHE9 |
| B | TRP10 |
| B | LEU11 |
| B | LYS120 |
| B | HOH615 |
| B | HOH633 |
| B | HOH769 |
| site_id | AD2 |
| Number of Residues | 6 |
| Details | binding site for residue GOL B 505 |
| Chain | Residue |
| B | ASP164 |
| B | GLY165 |
| B | ILE166 |
| B | SER167 |
| B | HOH651 |
| B | HOH847 |
| site_id | AD3 |
| Number of Residues | 10 |
| Details | binding site for residue GOL B 506 |
| Chain | Residue |
| A | HOH636 |
| B | GLU227 |
| B | ARG237 |
| B | SER239 |
| B | GOL507 |
| B | HOH601 |
| B | HOH623 |
| B | HOH645 |
| B | HOH789 |
| B | HOH1015 |
| site_id | AD4 |
| Number of Residues | 12 |
| Details | binding site for residue GOL B 507 |
| Chain | Residue |
| A | GLU227 |
| A | HIS228 |
| A | TYR231 |
| A | HOH713 |
| A | HOH902 |
| B | SER224 |
| B | GLU227 |
| B | HIS228 |
| B | GOL506 |
| B | HOH601 |
| B | HOH873 |
| B | HOH880 |
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 | GLU412 | |
| A | GLU452 | |
| B | ASP276 | |
| B | ASP287 | |
| B | HIS370 | |
| B | GLU412 |
| site_id | SWS_FT_FI3 |
| Number of Residues | 2 |
| Details | MOD_RES: Phosphoserine => ECO:0007744|PubMed:24275569 |
| Chain | Residue | Details |
| A | SER167 | |
| B | SER167 |
Catalytic Information from CSA
| site_id | MCSA1 |
| Number of Residues | 8 |
| Details | M-CSA 1001 |
| Chain | Residue | Details |
| A | HIS255 | hydrogen bond donor |
| A | ASP276 | metal ligand |
| A | ASP287 | metal ligand |
| A | HIS370 | metal ligand |
| A | HIS377 | hydrogen bond donor |
| A | ARG398 | hydrogen bond donor |
| A | GLU412 | metal ligand, proton acceptor, proton donor |
| A | GLU452 | metal ligand |
