3PW3
Crystal structure of a cysteine protease (BDI_2249) from Parabacteroides distasonis ATCC 8503 at 2.23 A resolution
Functional Information from GO Data
| Chain | GOid | namespace | contents |
| A | 0004177 | molecular_function | aminopeptidase activity |
| A | 0005737 | cellular_component | cytoplasm |
| A | 0006508 | biological_process | proteolysis |
| A | 0008234 | molecular_function | cysteine-type peptidase activity |
| A | 0009636 | biological_process | response to toxic substance |
| A | 0043418 | biological_process | homocysteine catabolic process |
| A | 0046872 | molecular_function | metal ion binding |
| A | 0070005 | molecular_function | cysteine-type aminopeptidase activity |
| B | 0004177 | molecular_function | aminopeptidase activity |
| B | 0005737 | cellular_component | cytoplasm |
| B | 0006508 | biological_process | proteolysis |
| B | 0008234 | molecular_function | cysteine-type peptidase activity |
| B | 0009636 | biological_process | response to toxic substance |
| B | 0043418 | biological_process | homocysteine catabolic process |
| B | 0046872 | molecular_function | metal ion binding |
| B | 0070005 | molecular_function | cysteine-type aminopeptidase activity |
| C | 0004177 | molecular_function | aminopeptidase activity |
| C | 0005737 | cellular_component | cytoplasm |
| C | 0006508 | biological_process | proteolysis |
| C | 0008234 | molecular_function | cysteine-type peptidase activity |
| C | 0009636 | biological_process | response to toxic substance |
| C | 0043418 | biological_process | homocysteine catabolic process |
| C | 0046872 | molecular_function | metal ion binding |
| C | 0070005 | molecular_function | cysteine-type aminopeptidase activity |
| D | 0004177 | molecular_function | aminopeptidase activity |
| D | 0005737 | cellular_component | cytoplasm |
| D | 0006508 | biological_process | proteolysis |
| D | 0008234 | molecular_function | cysteine-type peptidase activity |
| D | 0009636 | biological_process | response to toxic substance |
| D | 0043418 | biological_process | homocysteine catabolic process |
| D | 0046872 | molecular_function | metal ion binding |
| D | 0070005 | molecular_function | cysteine-type aminopeptidase activity |
| E | 0004177 | molecular_function | aminopeptidase activity |
| E | 0005737 | cellular_component | cytoplasm |
| E | 0006508 | biological_process | proteolysis |
| E | 0008234 | molecular_function | cysteine-type peptidase activity |
| E | 0009636 | biological_process | response to toxic substance |
| E | 0043418 | biological_process | homocysteine catabolic process |
| E | 0046872 | molecular_function | metal ion binding |
| E | 0070005 | molecular_function | cysteine-type aminopeptidase activity |
| F | 0004177 | molecular_function | aminopeptidase activity |
| F | 0005737 | cellular_component | cytoplasm |
| F | 0006508 | biological_process | proteolysis |
| F | 0008234 | molecular_function | cysteine-type peptidase activity |
| F | 0009636 | biological_process | response to toxic substance |
| F | 0043418 | biological_process | homocysteine catabolic process |
| F | 0046872 | molecular_function | metal ion binding |
| F | 0070005 | molecular_function | cysteine-type aminopeptidase activity |
Functional Information from PDB Data
| site_id | AC1 |
| Number of Residues | 4 |
| Details | BINDING SITE FOR RESIDUE ZN A 406 |
| Chain | Residue |
| A | CYS56 |
| A | HIS340 |
| C | ASP298 |
| C | HOH2426 |
| site_id | AC2 |
| Number of Residues | 4 |
| Details | BINDING SITE FOR RESIDUE ZN B 406 |
| Chain | Residue |
| B | CYS56 |
| B | HIS340 |
| B | CL417 |
| B | ACT441 |
| site_id | AC3 |
| Number of Residues | 4 |
| Details | BINDING SITE FOR RESIDUE ZN C 406 |
| Chain | Residue |
| C | HIS340 |
| E | ASP298 |
| E | CL419 |
| C | CYS56 |
| site_id | AC4 |
| Number of Residues | 4 |
| Details | BINDING SITE FOR RESIDUE ZN D 406 |
| Chain | Residue |
| B | ASP298 |
| B | CL422 |
| D | CYS56 |
| D | HIS340 |
| site_id | AC5 |
| Number of Residues | 4 |
| Details | BINDING SITE FOR RESIDUE ZN E 406 |
| Chain | Residue |
| E | CYS56 |
| E | HIS340 |
| E | CL420 |
| E | HOH590 |
| site_id | AC6 |
| Number of Residues | 4 |
| Details | BINDING SITE FOR RESIDUE ZN F 406 |
| Chain | Residue |
| F | CYS56 |
| F | HIS340 |
| F | CL418 |
| F | ACT442 |
| site_id | AC7 |
| Number of Residues | 6 |
| Details | BINDING SITE FOR RESIDUE K A 407 |
| Chain | Residue |
| A | ASP271 |
| A | SER273 |
| A | GLU274 |
| A | GLU335 |
| A | HOH596 |
| A | HOH637 |
| site_id | AC8 |
| Number of Residues | 6 |
| Details | BINDING SITE FOR RESIDUE K A 408 |
| Chain | Residue |
| A | ASP78 |
| A | LEU79 |
| A | GLU81 |
| A | GLU126 |
| A | HOH623 |
| A | HOH870 |
| site_id | AC9 |
| Number of Residues | 6 |
| Details | BINDING SITE FOR RESIDUE K D 409 |
| Chain | Residue |
| D | ASP78 |
| D | LEU79 |
| D | GLU81 |
| D | GLU126 |
| D | HOH888 |
| D | HOH1447 |
| site_id | BC1 |
| Number of Residues | 6 |
| Details | BINDING SITE FOR RESIDUE K B 410 |
| Chain | Residue |
| B | ASP78 |
| B | LEU79 |
| B | GLU81 |
| B | GLU126 |
| B | HOH578 |
| B | HOH689 |
| site_id | BC2 |
| Number of Residues | 5 |
| Details | BINDING SITE FOR RESIDUE K D 411 |
| Chain | Residue |
| D | ASP271 |
| D | SER273 |
| D | GLU274 |
| D | GLU335 |
| D | HOH1382 |
| site_id | BC3 |
| Number of Residues | 6 |
| Details | BINDING SITE FOR RESIDUE K C 412 |
| Chain | Residue |
| C | ASP271 |
| C | SER273 |
| C | GLU274 |
| C | GLU335 |
| C | HOH1589 |
| C | HOH1840 |
| site_id | BC4 |
| Number of Residues | 5 |
| Details | BINDING SITE FOR RESIDUE K F 413 |
| Chain | Residue |
| F | ASP271 |
| F | SER273 |
| F | GLU274 |
| F | GLU335 |
| F | HOH1591 |
| site_id | BC5 |
| Number of Residues | 6 |
| Details | BINDING SITE FOR RESIDUE K C 414 |
| Chain | Residue |
| C | ASP78 |
| C | LEU79 |
| C | GLU81 |
| C | GLU126 |
| C | HOH1169 |
| C | HOH1724 |
| site_id | BC6 |
| Number of Residues | 6 |
| Details | BINDING SITE FOR RESIDUE K E 415 |
| Chain | Residue |
| E | ASP78 |
| E | LEU79 |
| E | GLU81 |
| E | GLU126 |
| E | HOH541 |
| E | HOH1034 |
| site_id | BC7 |
| Number of Residues | 6 |
| Details | BINDING SITE FOR RESIDUE K F 416 |
| Chain | Residue |
| F | ASP78 |
| F | LEU79 |
| F | GLU81 |
| F | GLU126 |
| F | HOH916 |
| F | HOH984 |
| site_id | BC8 |
| Number of Residues | 4 |
| Details | BINDING SITE FOR RESIDUE CL B 417 |
| Chain | Residue |
| B | HIS340 |
| B | ASN361 |
| B | TRP363 |
| B | ZN406 |
| site_id | BC9 |
| Number of Residues | 4 |
| Details | BINDING SITE FOR RESIDUE CL F 418 |
| Chain | Residue |
| F | HIS340 |
| F | TRP363 |
| F | ZN406 |
| F | ACT442 |
| site_id | CC1 |
| Number of Residues | 3 |
| Details | BINDING SITE FOR RESIDUE CL E 419 |
| Chain | Residue |
| C | HIS340 |
| C | ZN406 |
| E | TRP302 |
| site_id | CC2 |
| Number of Residues | 4 |
| Details | BINDING SITE FOR RESIDUE CL E 420 |
| Chain | Residue |
| E | HIS340 |
| E | ASN361 |
| E | TRP363 |
| E | ZN406 |
| site_id | CC3 |
| Number of Residues | 1 |
| Details | BINDING SITE FOR RESIDUE CL A 421 |
| Chain | Residue |
| A | LYS377 |
| site_id | CC4 |
| Number of Residues | 3 |
| Details | BINDING SITE FOR RESIDUE CL B 422 |
| Chain | Residue |
| D | HIS340 |
| D | ZN406 |
| B | TRP302 |
| site_id | CC5 |
| Number of Residues | 1 |
| Details | BINDING SITE FOR RESIDUE CL B 423 |
| Chain | Residue |
| B | ASN49 |
| site_id | CC6 |
| Number of Residues | 1 |
| Details | BINDING SITE FOR RESIDUE CL E 424 |
| Chain | Residue |
| E | ASN49 |
| site_id | CC7 |
| Number of Residues | 3 |
| Details | BINDING SITE FOR RESIDUE CL F 425 |
| Chain | Residue |
| F | ALA171 |
| F | MSE172 |
| F | HOH1013 |
| site_id | CC8 |
| Number of Residues | 3 |
| Details | BINDING SITE FOR RESIDUE CL D 426 |
| Chain | Residue |
| D | ALA171 |
| D | MSE172 |
| D | HOH2022 |
| site_id | CC9 |
| Number of Residues | 2 |
| Details | BINDING SITE FOR RESIDUE CL B 427 |
| Chain | Residue |
| B | ALA171 |
| B | MSE172 |
| site_id | DC1 |
| Number of Residues | 6 |
| Details | BINDING SITE FOR RESIDUE EDO A 428 |
| Chain | Residue |
| A | TYR112 |
| A | ASN238 |
| A | ASN386 |
| A | HOH473 |
| A | HOH1018 |
| A | HOH1353 |
| site_id | DC2 |
| Number of Residues | 7 |
| Details | BINDING SITE FOR RESIDUE EDO F 429 |
| Chain | Residue |
| F | PHE111 |
| F | TYR112 |
| F | SER218 |
| F | ASN238 |
| F | ASN386 |
| F | HOH514 |
| F | HOH1899 |
| site_id | DC3 |
| Number of Residues | 6 |
| Details | BINDING SITE FOR RESIDUE EDO F 430 |
| Chain | Residue |
| F | GLY109 |
| F | PHE111 |
| F | ASP339 |
| F | GLY341 |
| F | ASN386 |
| F | HOH1451 |
| site_id | DC4 |
| Number of Residues | 9 |
| Details | BINDING SITE FOR RESIDUE EDO A 431 |
| Chain | Residue |
| A | PHE34 |
| A | VAL284 |
| A | LEU312 |
| A | LYS315 |
| A | PRO316 |
| A | GLN317 |
| A | GLN319 |
| A | TYR356 |
| A | HOH2285 |
| site_id | DC5 |
| Number of Residues | 5 |
| Details | BINDING SITE FOR RESIDUE EDO C 432 |
| Chain | Residue |
| C | GLY109 |
| C | SER110 |
| C | PHE111 |
| C | ASP339 |
| C | ASN386 |
| site_id | DC6 |
| Number of Residues | 5 |
| Details | BINDING SITE FOR RESIDUE EDO B 433 |
| Chain | Residue |
| B | SER110 |
| B | PHE111 |
| B | ASP339 |
| B | GLY341 |
| B | ASN386 |
| site_id | DC7 |
| Number of Residues | 9 |
| Details | BINDING SITE FOR RESIDUE EDO A 434 |
| Chain | Residue |
| A | TRP57 |
| A | GLY109 |
| A | ASP339 |
| A | GLY341 |
| A | ASN386 |
| A | HOH817 |
| A | HOH1299 |
| A | HOH1353 |
| A | HOH2019 |
| site_id | DC8 |
| Number of Residues | 3 |
| Details | BINDING SITE FOR RESIDUE EDO A 435 |
| Chain | Residue |
| A | LYS48 |
| A | ASN49 |
| A | HOH1525 |
| site_id | DC9 |
| Number of Residues | 4 |
| Details | BINDING SITE FOR RESIDUE EDO A 436 |
| Chain | Residue |
| A | LYS196 |
| B | TYR369 |
| B | TYR374 |
| B | HOH852 |
| site_id | EC1 |
| Number of Residues | 6 |
| Details | BINDING SITE FOR RESIDUE EDO D 437 |
| Chain | Residue |
| D | TRP57 |
| D | GLY109 |
| D | PHE111 |
| D | ASP339 |
| D | GLY341 |
| D | ASN386 |
| site_id | EC2 |
| Number of Residues | 7 |
| Details | BINDING SITE FOR RESIDUE EDO A 438 |
| Chain | Residue |
| A | TYR369 |
| A | TYR374 |
| A | HOH712 |
| A | HOH1853 |
| A | HOH1947 |
| B | LYS196 |
| B | EDO439 |
| site_id | EC3 |
| Number of Residues | 6 |
| Details | BINDING SITE FOR RESIDUE EDO B 439 |
| Chain | Residue |
| A | THR38 |
| A | GLU41 |
| A | EDO438 |
| B | GLU76 |
| B | TYR195 |
| B | LYS196 |
| site_id | EC4 |
| Number of Residues | 5 |
| Details | BINDING SITE FOR RESIDUE EDO C 440 |
| Chain | Residue |
| C | TYR112 |
| C | GLY242 |
| C | MSE243 |
| C | HOH1768 |
| C | HOH1936 |
| site_id | EC5 |
| Number of Residues | 5 |
| Details | BINDING SITE FOR RESIDUE ACT B 441 |
| Chain | Residue |
| B | GLN50 |
| B | CYS56 |
| B | HIS340 |
| B | TRP363 |
| B | ZN406 |
| site_id | EC6 |
| Number of Residues | 9 |
| Details | BINDING SITE FOR RESIDUE ACT F 442 |
| Chain | Residue |
| F | GLN50 |
| F | GLY54 |
| F | CYS56 |
| F | HIS340 |
| F | TRP363 |
| F | ZN406 |
| F | CL418 |
| F | HOH2340 |
| F | HOH2353 |
Functional Information from PROSITE/UniProt
| site_id | PS00139 |
| Number of Residues | 12 |
| Details | THIOL_PROTEASE_CYS Eukaryotic thiol (cysteine) proteases cysteine active site. QNrAGTCWCySS |
| Chain | Residue | Details |
| A | GLN50-SER61 |
